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Wang, Jiangshan; Wang, Chunting; Yang, Qiwen; Xu, Yingchun; Xu, Jun; Li, Yi; Yu, Xuezhong; Zhu, Huadong; Liu, Jihai title: Characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in Beijing date: 2020-05-07 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.008 sha: doc_id: 274845 cord_uid: pqvlh3eg file: cache/cord-282360-byqhzyzi.json key: cord-282360-byqhzyzi authors: Zhang, Dingmei; Lu, Jiayuan; Lu, Jiahai title: Enterovirus 71 vaccine: close but still far date: 2010-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2009.12.002 sha: doc_id: 282360 cord_uid: byqhzyzi file: cache/cord-283590-xvnv17zy.json key: cord-283590-xvnv17zy authors: Chen, Dabiao; Xu, Wenxiong; Lei, Ziying; Huang, Zhanlian; Liu, Jing; Gao, Zhiliang; Peng, Liang title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.003 sha: doc_id: 283590 cord_uid: xvnv17zy file: cache/cord-262310-z0m6uuzf.json key: cord-262310-z0m6uuzf authors: Effenberger, Maria; 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Costa, Aldo F.; Mera, Robertino M.; Recalde, Bettsy Y.; Bustos, Javier A.; García, Héctor H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.003 sha: doc_id: 274028 cord_uid: dvsvtsn0 file: cache/cord-289304-9srk0ohb.json key: cord-289304-9srk0ohb authors: Bagnato, Sergio; Boccagni, Cristina; Marino, Giorgio; Prestandrea, Caterina; D’Agostino, Tiziana; Rubino, Francesca title: Critical illness myopathy after COVID-19 date: 2020-08-05 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.072 sha: doc_id: 289304 cord_uid: 9srk0ohb file: cache/cord-304743-0bsdahh6.json key: cord-304743-0bsdahh6 authors: Kortepeter, Mark G; Dierberg, Kerry; Shenoy, Erica S; Cieslak, Theodore J; Bhadelia, Nahid; Davey, Richard T; Evans, Jared D; Frank, Maria G; Grein, Jonathan; Kraft, Colleen S; Kratochvil, Chris J; Martins, Karen; McLellan, Susan; Measer, Greg; Mehta, Aneesh K; Raabe, Vanessa; Risi, George; Sauer, Lauren; Uyeki, Timothy title: Marburg Virus Disease: a Summary for Clinicians date: 2020-08-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.042 sha: doc_id: 304743 cord_uid: 0bsdahh6 file: cache/cord-305782-gnzwe2z2.json key: cord-305782-gnzwe2z2 authors: Satici, Celal; Demirkol, Mustafa Asim; Altunok, Elif Sargin; Gursoy, Bengul; Alkan, Mustafa; Kamat, Sadettin; Demirok, Berna; Surmeli, Cemile Dilsah; Calik, Mustafa; Cavus, Zuhal; Esatoglu, Sinem Nihal title: Performance of Pneumonia Severity Index and CURB-65 in Predicting 30-day mortality in patients with COVID-19 date: 2020-06-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.038 sha: doc_id: 305782 cord_uid: gnzwe2z2 file: cache/cord-311413-uiwjrvru.json key: cord-311413-uiwjrvru authors: Chanda-Kapata, Pascalina; Kapata, Nathan; Zumla, Alimuddin title: COVID-19 and malaria: A symptom screening challenge for malaria endemic countries date: 2020-04-27 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.007 sha: doc_id: 311413 cord_uid: uiwjrvru file: cache/cord-257737-obadq502.json key: cord-257737-obadq502 authors: Wu, Di; Lu, Jianyun; Liu, Yanhui; Zhang, Zhoubin; Luo, Lei title: Positive effects of COVID-19 control measures on influenza prevention date: 2020-04-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.009 sha: doc_id: 257737 cord_uid: obadq502 file: cache/cord-311026-mpr3xb2a.json key: cord-311026-mpr3xb2a authors: Petersen, Eskild; Wasserman, Sean; Lee, Shui-Shan; GO, Unyeong; Holmes, Allison H.; Abri, Seif Al; McLellan, Susan; Blumberg, Lucille; Tambyah, Paul title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.035 sha: doc_id: 311026 cord_uid: mpr3xb2a file: cache/cord-259837-5tbdqzxr.json key: cord-259837-5tbdqzxr authors: Kalcioglu, Mahmut Tayyar; Cag, Yasemin; Kilic, Osman; Tuysuz, Ozan title: May COVID-19 cause sudden sensorineural hearing loss? date: 2020-09-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1468 sha: doc_id: 259837 cord_uid: 5tbdqzxr file: cache/cord-276445-m5vjo3ym.json key: cord-276445-m5vjo3ym authors: Lee, Hyojung; 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Togashi, Yuki; Fujimori, Daiki; Kaizuka, Haruki; Otsuki, Shunsuke; Wada, Takuya; Takeuchi, Yoshikazu; Abe, Shinji title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases date: 2020-09-28 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1450 sha: doc_id: 293942 cord_uid: n5ypkftc file: cache/cord-304872-hnxmtbrf.json key: cord-304872-hnxmtbrf authors: Lv, Hao; Zhang, Wei; Zhu, Zhanyong; Xiong, Qiutang; Xiang, Rong; Wang, Yingying; Shi, Wendan; Deng, Zhifeng; Xu, Yu title: Prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with COVID‑19 in Wuhan, China date: 2020-09-17 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.039 sha: doc_id: 304872 cord_uid: hnxmtbrf file: cache/cord-273090-fdzkfo1u.json key: cord-273090-fdzkfo1u authors: He, Susu; Zhou, Chao; Lu, Dongqing; Yang, Haihua; XU, Hailing; Wu, Guixian; Pan, Weijia; Zhu, Rui; Jia, HaiJian; Tang, Xinni; Chen, Xi; Wu, Xiaomai title: Relationship between Chest CT manifestations and immune response in COVID-19 patients date: 2020-06-20 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.059 sha: doc_id: 273090 cord_uid: fdzkfo1u file: cache/cord-293630-zc8huo1j.json key: cord-293630-zc8huo1j authors: Capone, Alessandro title: Simultaneous circulation of COVID-19 and flu in Italy: potential combined effects on the risk of death? date: 2020-08-05 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.077 sha: doc_id: 293630 cord_uid: zc8huo1j file: cache/cord-306200-d5qn65k0.json key: cord-306200-d5qn65k0 authors: Petersen, Eskild; McCloskey, Brian; Hui, David S; Kock, Richard; Ntoumi, Francine; Memish, Ziad A; Kapata, Nathan; Azhar, Esam I; Pollack, Marjorie; Madoff, Larry C.; Hamer, Davidson H; Nachega, Jean B; Pshenichnaya, N.; Zumla, Alimuddin title: COVID-19 travel restrictions and the International Health Regulations – call for an open debate on easing of travel restrictions date: 2020-04-17 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.029 sha: doc_id: 306200 cord_uid: d5qn65k0 file: cache/cord-311453-l6quzef6.json key: cord-311453-l6quzef6 authors: Klopfenstein, Timothée; Zayet, Souheil; Lohse, Anne; Selles, Phillippe; Zahra, Hajer; Kadiane-Oussou, N’dri Juliette; Toko, Lynda; Royer, Pierre-Yves; Balblanc, Jean-Charles; Gendrin, Vincent; Conrozier, Thierry title: Impact of Tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 COVID-19 patients date: 2020-08-13 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.024 sha: doc_id: 311453 cord_uid: l6quzef6 file: cache/cord-311479-8pjoz64q.json key: cord-311479-8pjoz64q authors: He, Daihai; Zhao, Shi; Lin, Qianying; Zhuang, Zian; Cao, Peihua; Wang, Maggie H; Yang, Lin title: The relative transmissibility of asymptomatic cases among close contacts date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.034 sha: doc_id: 311479 cord_uid: 8pjoz64q file: cache/cord-308114-68cgub5o.json key: cord-308114-68cgub5o authors: Afrin, Lawrence B.; Weinstock, Leonard B.; Molderings, Gerhard J. title: Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome date: 2020-09-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.016 sha: doc_id: 308114 cord_uid: 68cgub5o file: cache/cord-257265-lkzytud0.json key: cord-257265-lkzytud0 authors: Zheng, Fang; Zhou, Yanwen; Zhou, Zhiguo; Ye, Fei; Huang, Baoying; Huang, Yaxiong; Ma, Jing; Zuo, Qi; Tan, Xin; Xie, Jun; Niu, Peihua; Wang, Wenlong; Xu, Yun; Peng, Feng; Zhou, Ning; Cai, Chunlin; Tang, Wei; Xiao, Xinqiang; Li, Yi; Zhou, Zhiguang; Jiang, Yongfang; Xie, Yuanlin; Tan, Wenjie; Gong, Guozhong title: SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date: 2020-08-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.053 sha: doc_id: 257265 cord_uid: lkzytud0 file: cache/cord-277640-vy7ex5lv.json key: cord-277640-vy7ex5lv authors: Calderaro, Adriana; 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Wang, Jui-Hsiang; Hsueh, Po-Ren title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.011 sha: doc_id: 305763 cord_uid: 160heazx file: cache/cord-292256-jp80u828.json key: cord-292256-jp80u828 authors: Moriguchi, Takeshi; Harii, Norikazu; Goto, Junko; Harada, Daiki; Sugawara, Hisanori; Takamino, Junichi; Ueno, Masateru; Sakata, Hiroki; Kondo, Kengo; Myose, Natsuhiko; Nakao, Atsuhito; Takeda, Masayuki; Haro, Hirotaka; Inoue, Osamu; Suzuki-Inoue, Katsue; Kubokawa, Kayo; Ogihara, Shinji; Sasaki, Tomoyuki; Kinouchi, Hiroyuki; Kojin, Hiroyuki; Ito, Masami; Onishi, Hiroshi; Shimizu, Tatsuya; Sasaki, Yu; Enomoto, Nobuyuki; Ishihara, Hiroshi; Furuya, Shiomi; Yamamoto, Tomoko; Shimada, Shinji title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.062 sha: doc_id: 292256 cord_uid: jp80u828 file: cache/cord-293247-ltxt2dfv.json key: cord-293247-ltxt2dfv authors: Elachola, Habida; Assiri, Abdullah; Turkestani, Abdual Hafiz; Sow, Samba S.; Petersen, Eskild; Al-Tawfiq, Jaffar A.; Memish, Ziad A. title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings date: 2015-10-09 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2015.10.003 sha: doc_id: 293247 cord_uid: ltxt2dfv file: cache/cord-300774-5mrkmctl.json key: cord-300774-5mrkmctl authors: Hernández-Mora, Miguel Górgolas; Cabello Úbeda, Alfonso; Pérez, Laura Prieto; Álvarez, Felipe Villar; Álvarez, Beatriz Álvarez; Rodríguez Nieto, María Jesús; Acosta, Irene Carrillo; Ormaechea, Itziar Fernández; Al-Hayani, Aws Waleed Mohammed; Carballosa, Pilar; Martínez, Silvia Calpena; Ezzine, Farah; González, Marina Castellanos; Naya, Alba; de las Heras, Marta López; Rodríguez Guzmán, Marcel José; Guijarro, Ana Cordero; Lavado, Antonio Broncano; Valcayo, Alicia Macías; García, Marta Martín; Martínez, Javier Bécares; Roblas, Ricardo Fernández; Piris Pinilla, Miguel Ángel; Alen, José Fortes; Pernaute, Olga Sánchez; Bueno, Fredeswinda Romero; Frades, Sarah Heili; Romero, Germán Peces Barba title: Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date: 2020-10-25 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.045 sha: doc_id: 300774 cord_uid: 5mrkmctl file: cache/cord-302409-40ktyt5q.json key: cord-302409-40ktyt5q authors: Wang, Jie; Feng, Haiting; Zhang, Sheng; Ni, Zuowei; Ni, Lingmei; Chen, Yu; Zhuo, Lixin; Zhong, Zifeng; Qu, Tingting title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.024 sha: doc_id: 302409 cord_uid: 40ktyt5q file: cache/cord-315059-l6guql8q.json key: cord-315059-l6guql8q authors: Mubarak, Naeem title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. Time for some unpopular decisions date: 2020-04-30 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.067 sha: doc_id: 315059 cord_uid: l6guql8q file: cache/cord-315860-9j667c03.json key: cord-315860-9j667c03 authors: Jullien, Sophie; Pradhan, Dinesh; Tshering, Tashi; Sharma, Ragunath; Dema, Kumbu; Garcia-Garcia, Selene; Ribó, Jose Luis; Muñoz-Almagro, Carmen; Bassat, Quique title: Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study date: 2020-04-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.017 sha: doc_id: 315860 cord_uid: 9j667c03 file: cache/cord-284652-7npya3yx.json key: cord-284652-7npya3yx authors: Shim, Eunha; Tariq, Amna; Chowell, Gerardo title: Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020 date: 2020-10-08 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.007 sha: doc_id: 284652 cord_uid: 7npya3yx file: cache/cord-316505-tdlj5smv.json key: cord-316505-tdlj5smv authors: Kumar, Abhai; Singh, Smita; Ahirwar, Suneel Kumar; Nath, Gopal title: Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers date: 2013-11-28 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2013.10.008 sha: doc_id: 316505 cord_uid: tdlj5smv file: cache/cord-317399-693q80xo.json key: cord-317399-693q80xo authors: Al Wahaibi, Adil; Al Manji, Abdullah; Al Maani, Amal; Al Rawahi, Bader; Al Harthy, Khalid; Alyaquobi, Fatma; Al-Jardani, Amina; Petersen, Eskild; Al-Abri, Seif title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date: 2020-08-20 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.039 sha: doc_id: 317399 cord_uid: 693q80xo file: cache/cord-317624-qdzhncs0.json key: cord-317624-qdzhncs0 authors: Choi, Min Joo; Kang, Minsun; Shin, So Youn; Noh, Ji Yun; Cheong, Hee Jin; Kim, Woo Joo; Jung, Jaehun; Song, Joon Young title: Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study date: 2020-10-27 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.062 sha: doc_id: 317624 cord_uid: qdzhncs0 file: cache/cord-317500-ufo2qgj4.json key: cord-317500-ufo2qgj4 authors: Scialpi, Michele; Scialp, Sara; Piscioli, Irene; Scalera, Giovanni; Longo, Fernando title: Pulmonary thromboembolism in criticall ill COVID-19 patients date: 2020-04-24 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.056 sha: doc_id: 317500 cord_uid: ufo2qgj4 file: cache/cord-311654-ixn65hxb.json key: cord-311654-ixn65hxb authors: Zumla, Alimuddin; Azhar, Esam I.; Shafi, Shuja; Memish, Ziad A. title: COVID-19 and the scaled-down 2020 Hajj Pilgrimage - Decisive, logical and prudent decision making by Saudi authorities overcomes pre-Hajj public health concerns date: 2020-08-08 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.014 sha: doc_id: 311654 cord_uid: ixn65hxb file: cache/cord-317080-kn56oov6.json key: cord-317080-kn56oov6 authors: Quadri, Sayed. 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Almasri, Malak; Turkestani, Abdulhafeez; Al-Shangiti, Ali M.; Yezli, Saber title: Etiology of severe community-acquired pneumonia during the 2013 Hajj—part of the MERS-CoV surveillance program date: 2014-06-23 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2014.06.003 sha: doc_id: 318315 cord_uid: r6wqywwe file: cache/cord-318808-1cfwj5uq.json key: cord-318808-1cfwj5uq authors: Li, Ying; Wang, Haizhou; Wang, Fan; Du, Hui; Liu, Xueru; Chen, Peng; Wang, Yanli; Lu, Xiaoxia title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years date: 2020-06-12 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.026 sha: doc_id: 318808 cord_uid: 1cfwj5uq file: cache/cord-320860-qt84oicg.json key: cord-320860-qt84oicg authors: Zhang, Aining; Leng, Yan; Zhang, Yi; Wu, Kefan; Ji, Yelong; Lei, Shaoqing; Xia, Zhongyuan title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date: 2020-09-15 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.021 sha: doc_id: 320860 cord_uid: qt84oicg file: cache/cord-319814-tyqb473m.json key: cord-319814-tyqb473m authors: Zhang, Dingmei; He, Zhenjian; Xu, Lin; Zhu, Xun; Wu, Jueheng; Wen, Weitao; Zheng, Yun; Deng, Yu; Chen, Jieling; Hu, Yiwen; Li, Mengfeng; Cao, Kaiyuan title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2014.02.019 sha: doc_id: 319814 cord_uid: tyqb473m file: cache/cord-320829-uepneyug.json key: cord-320829-uepneyug authors: He, Zhongping; Zhao, Chunhui; Dong, Qingming; Zhuang, Hui; Song, Shujing; Peng, Guoai; Dwyer, Dominic E. title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2004.07.014 sha: doc_id: 320829 cord_uid: uepneyug file: cache/cord-320902-1hfxju5f.json key: cord-320902-1hfxju5f authors: Filocamo, Giovanni; Mangioni, Davide; Tagliabue, Paola; Aliberti, Stefano; Costantino, Giorgio; Minoia, Francesca; Bandera, Alessandra title: Use of anakinra in severe COVID-19: a case report date: 2020-05-11 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.026 sha: doc_id: 320902 cord_uid: 1hfxju5f file: cache/cord-318181-xxc7vdnt.json key: cord-318181-xxc7vdnt authors: Ahmed, Anwar E.; Al-Jahdali, Hamdan; Alshukairi, Abeer N.; Alaqeel, Mody; Siddiq, Salma S.; Alsaab, Hanan; Sakr, Ezzeldin A.; Alyahya, Hamed A.; Alandonisi, Munzir M.; Subedar, Alaa T.; Aloudah, Nouf M.; Baharoon, Salim; Alsalamah, Majid A.; Al Johani, Sameera; Alghamdi, Mohammed G. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2018.03.005 sha: doc_id: 318181 cord_uid: xxc7vdnt file: cache/cord-324231-nik7xizn.json key: cord-324231-nik7xizn authors: Aitsi-Selmi, Amina; Murray, Virginia; Heymann, David; McCloskey, Brian; Azhar, Esam I.; Petersen, Eskild; Zumla, Alimuddin; Dar, Osman title: Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction date: 2016-04-07 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2016.04.006 sha: doc_id: 324231 cord_uid: nik7xizn file: cache/cord-320785-42p8292o.json key: cord-320785-42p8292o authors: Lobo, Andréa de Paula; Cardoso-dos-Santos, Augusto César; Rocha, Marli Souza; Pinheiro, Rejane Sobrino; Bremm, João Matheus; Macário, Eduardo Marques; Oliveira, Wanderson Klébler de; França, Giovanny Vinícius Araújo de title: COVID-19 epidemic in Brazil: where we at? date: 2020-06-16 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.044 sha: doc_id: 320785 cord_uid: 42p8292o file: cache/cord-323455-26xi2lqf.json key: cord-323455-26xi2lqf authors: AlBarrak, Ali; Alotaibi, Badriah; Yassin, Yara; Mushi, Abdulaziz; Maashi, Fuad; Seedahmed, Yassein; Alshaer, Mohamed; Altaweel, Abdulaziz; Elshiekh, Husameddin; Turkistani, Abdulhafiz; Petigara, Tanaz; Grabenstein, John; Yezli, Saber title: Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date: 2018-02-21 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2018.02.008 sha: doc_id: 323455 cord_uid: 26xi2lqf file: cache/cord-323696-0lq8ql6n.json key: cord-323696-0lq8ql6n authors: Bearman, Gonzalo; 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Eren, Neriman; Heuser, Isabella; Hellmann-Regen, Julian title: A Simple Approach to Optimum Pool Size for Pooled SARS-CoV-2 Testing date: 2020-08-28 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.063 sha: doc_id: 338576 cord_uid: gh1plurq file: cache/cord-325325-xw7627x9.json key: cord-325325-xw7627x9 authors: Skeik, Nedaa; Jabr, Fadi I. title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2007.07.002 sha: doc_id: 325325 cord_uid: xw7627x9 file: cache/cord-324295-9c1zxjng.json key: cord-324295-9c1zxjng authors: Bonilla-Aldana, D. Katterine; Jimenez-Diaz, S. Daniela; Arango-Duque, J. Sebastian; Aguirre-Florez, Mateo; Balbin-Ramon, Graciela J.; Paniz-Mondolfi, Alberto; Suárez, Jose Antonio; Pachar, Monica R.; Perez-Garcia, Luis A.; Delgado-Noguera, Lourdes A.; Sierra, Manuel Antonio; Muñoz-Lara, Fausto; Zambrano, Lysien I.; Rodriguez-Morales, Alfonso J. title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.050 sha: doc_id: 324295 cord_uid: 9c1zxjng file: cache/cord-340279-bq5owwot.json key: cord-340279-bq5owwot authors: Espíndola, Otávio de Melo; Siqueira, Marilda; Soares, Cristiane Nascimento; Lima, Marco Antonio Sales Dantas de; Leite, Ana Claudia Celestino Bezerra; Araujo, Abelardo Queiroz Campos; Brandão, Carlos Otávio; Silva, Marcus Tulius Teixeira title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date: 2020-06-04 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.123 sha: doc_id: 340279 cord_uid: bq5owwot file: cache/cord-330692-rqwkkfp0.json key: cord-330692-rqwkkfp0 authors: He, Daihai; Shi, Zhao; Li, Yingke; Cao, Peihua; Gao, Daozhou; Lou, Yijun; Yang, Lin title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date: 2020-06-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.075 sha: doc_id: 330692 cord_uid: rqwkkfp0 file: cache/cord-343789-6tq0kcfd.json key: cord-343789-6tq0kcfd authors: Al-Tawfiq, Jaffar A.; Momattin, Hisham; Dib, Jean; Memish, Ziad A. title: Ribavirin and interferon therapy in patients infected with the Middle East respiratory syndrome coronavirus: an observational study date: 2014-01-06 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2013.12.003 sha: doc_id: 343789 cord_uid: 6tq0kcfd file: cache/cord-341775-mucatzaa.json key: cord-341775-mucatzaa authors: Shafi, Shuja; Dar, Osman; Khan, Mishal; Khan, Minal; Azhar, Esam I.; McCloskey, Brian; Zumla, Alimuddin; Petersen, Eskild title: The annual Hajj pilgrimage—minimizing the risk of ill health in pilgrims from Europe and opportunity for driving the best prevention and health promotion guidelines date: 2016-06-22 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2016.06.013 sha: doc_id: 341775 cord_uid: mucatzaa file: cache/cord-332348-yi85sfks.json key: cord-332348-yi85sfks authors: Liang, Yujie; Xu, Jiabin; Chu, Mei; Mai, Jianbo; Lai, Niangmei; Tang, Wen; Yang, Tuanjie; Zhang, Sien; Guan, Chenyu; Zhong, Fan; Yang, Liuping; Liao, Guiqing title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.086 sha: doc_id: 332348 cord_uid: yi85sfks file: cache/cord-346461-eqyte6ko.json key: cord-346461-eqyte6ko authors: Scialpi, Michele title: Pneumonia misinterpretation in COVID-19: revisitation and update date: 2020-08-28 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.067 sha: doc_id: 346461 cord_uid: eqyte6ko file: cache/cord-344478-5gp7v1uh.json key: cord-344478-5gp7v1uh authors: Rosenberg, Eli S.; Holtgrave, David R.; Udo, Tomoko title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 date: 2020-07-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.07.055 sha: doc_id: 344478 cord_uid: 5gp7v1uh file: cache/cord-345275-h0hvaxgx.json key: cord-345275-h0hvaxgx authors: Sun, Mengyao; Xu, Yinghui; He, Hua; Zhang, Li; Wang, Xu; Qiu, Qing; Sun, Chao; Guo, Ye; Qiu, Shi; Ma, Kewei title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.107 sha: doc_id: 345275 cord_uid: h0hvaxgx file: cache/cord-351740-779g8tr1.json key: cord-351740-779g8tr1 authors: Khaba, Moshawa Calvin; Ngale, Tshepo Cletus; Madala, Nomandla title: COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date: 2020-09-25 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1435 sha: doc_id: 351740 cord_uid: 779g8tr1 file: cache/cord-349418-98sgr5iv.json key: cord-349418-98sgr5iv authors: Bo, Yacong; Guo, Cui; Lin, Changqing; Zeng, Yiqian; Li, Hao Bi; Zhang, Yumiao; Hossain, Md Shakhaoat; Chan, Jimmy W.M.; Yeung, David W.; Kwok, Kin-on; Wong, Samuel Y.S.; Lau, Alexis K.H.; Lao, Xiang Qian title: Effectiveness of non-pharmaceutical interventions on COVID-19 transmission in 190 countries from 23 January to 13 April 2020 date: 2020-10-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.066 sha: doc_id: 349418 cord_uid: 98sgr5iv file: cache/cord-340410-s9haq8y1.json key: cord-340410-s9haq8y1 authors: Fukumoto, Tatsuya; Iwasaki, Sumio; Fujisawa, Shinichi; Hayasaka, Kasumi; Sato, Kaori; Oguri, Satoshi; Taki, Keisuke; Nakakubo, Sho; Kamada, Keisuke; Yamashita, Yu; Konno, Satoshi; Nishida, Mutsumi; Sugita, Junichi; Teshima, Takanori title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-06-26 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.074 sha: doc_id: 340410 cord_uid: s9haq8y1 file: cache/cord-355343-dtdsd8j2.json key: cord-355343-dtdsd8j2 authors: Buonsenso, Danilo; Cinicola, Bianca; Raffaelli, Francesca; Sollena, Pietro; Iodice, Francesco title: Social consequences of COVID-19 in a low resource setting in Sierra Leone, West Africa date: 2020-06-01 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.104 sha: doc_id: 355343 cord_uid: dtdsd8j2 file: cache/cord-347349-caz5fwl1.json key: cord-347349-caz5fwl1 authors: Yu, Xinhua; Duan, Jiasong; Jiang, Yu; Zhang, Hongmei title: Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea date: 2020-07-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.101 sha: doc_id: 347349 cord_uid: caz5fwl1 file: cache/cord-356074-kw8c2fgk.json key: cord-356074-kw8c2fgk authors: Oboh, Mary Aigbiremo; Omoleke, Semeeh Akinwale; Ajibola, Olumide; Manneh, Jarra; Kanteh, Abdoulie; Sesay, Abdul-Karim; Amambua-Ngwa, Alfred title: Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks date: 2020-08-13 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.08.027 sha: doc_id: 356074 cord_uid: kw8c2fgk file: cache/cord-354780-yzyixucr.json key: cord-354780-yzyixucr authors: Lin, Chih-Yen; Wang, Wen-Hung; Urbina, Aspiro Nayim; Tseng, Sung-Pin; Lu, Po-Liang; Chen, Yen-Hsu; Yu, Ming-Lung; Wang, Seng-Fan title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date: 2020-06-13 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.031 sha: doc_id: 354780 cord_uid: yzyixucr file: cache/cord-349645-6o8773c5.json key: cord-349645-6o8773c5 authors: Li, He; Xu, Xiao-Long; Dai, Da-Wei; Huang, Zhen-Yu; Ma, Zhuang; Guan, Yan-Jun title: Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date: 2020-06-02 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.076 sha: doc_id: 349645 cord_uid: 6o8773c5 file: cache/cord-323332-vu2cre8k.json key: cord-323332-vu2cre8k authors: Luo, Yang; He, Guo-Ping; Zhou, Jijan-Wei; Luo, Ying title: Factors impacting compliance with standard precautions in nursing, China date: 2010-11-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2009.03.037 sha: doc_id: 323332 cord_uid: vu2cre8k file: cache/cord-347907-0nrejsgr.json key: cord-347907-0nrejsgr authors: Alqahtani, Amani S.; Wiley, Kerrie E.; Tashani, Mohamed; Willaby, Harold W.; Heywood, Anita E.; BinDhim, Nasser F.; Booy, Robert; Rashid, Harunor title: Exploring barriers to and facilitators of preventive measures against infectious diseases among Australian Hajj pilgrims: cross-sectional studies before and after Hajj date: 2016-02-10 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2016.02.005 sha: doc_id: 347907 cord_uid: 0nrejsgr file: cache/cord-355480-mx9dbm73.json key: cord-355480-mx9dbm73 authors: Bajunirwe, Francis; Izudi, Jonathan; Asiimwe, Stephen title: Long distance truck drivers and the increasing risk of COVID-19 spread in Uganda date: 2020-06-29 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.085 sha: doc_id: 355480 cord_uid: mx9dbm73 file: cache/cord-347499-7q47jh14.json key: cord-347499-7q47jh14 authors: Burrel, Sonia; Hausfater, Pierre; Dres, Martin; Pourcher, Valérie; Luyt, Charles-Edouard; Teyssou, Elisa; Soulié, Cathia; Calvez, Vincent; Marcelin, Anne-Geneviève; Boutolleau, David title: Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date: 2020-10-25 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.10.040 sha: doc_id: 347499 cord_uid: 7q47jh14 file: cache/cord-321412-6g3obmzc.json key: cord-321412-6g3obmzc authors: Khamis, Faryal; Al-Zakwani, Ibrahim; Al Hashmi, Sabria; Al Dowaiki, Samata; Al Bahrani, Maher; Pandak, Nenad; Al Khalili, Huda; Memish, Ziad title: Therapeutic Plasma Exchange in Adults with Severe COVID-19 Infection date: 2020-06-23 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.06.064 sha: doc_id: 321412 cord_uid: 6g3obmzc Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-intJInfectDis-cord === file2bib.sh === id: cord-029882-kufs0fxe author: Malviya, Amit title: The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-029882-kufs0fxe.txt cache: ./cache/cord-029882-kufs0fxe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-029882-kufs0fxe.txt' === file2bib.sh === id: cord-282177-8l7zukg4 author: Lin, Yi-Chun title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-282177-8l7zukg4.txt cache: ./cache/cord-282177-8l7zukg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282177-8l7zukg4.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 52746 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 54227 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-258881-74aijckl author: Wang, Maomao title: Case Report: One Case of Coronavirus Desease 2019(COVID-19) in Patient Co-nfected by HIV With a Low CD4+ T Cell Count date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-258881-74aijckl.txt cache: ./cache/cord-258881-74aijckl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258881-74aijckl.txt' === file2bib.sh === id: cord-258078-k7y8k1vx author: Jang, Sukbin title: Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-258078-k7y8k1vx.txt cache: ./cache/cord-258078-k7y8k1vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258078-k7y8k1vx.txt' === file2bib.sh === id: cord-254776-m4makxr8 author: Luo, Shiua title: A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-254776-m4makxr8.txt cache: ./cache/cord-254776-m4makxr8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-254776-m4makxr8.txt' === file2bib.sh === id: cord-272015-1anph6qi author: Dauby, Nicolas title: The unfinished story of hydroxychloroquine in COVID-19: the right anti-inflammatory dose at the right moment? date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-272015-1anph6qi.txt cache: ./cache/cord-272015-1anph6qi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272015-1anph6qi.txt' === file2bib.sh === id: cord-272179-wvw5mmy3 author: Calderaro, Adriana title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-272179-wvw5mmy3.txt cache: ./cache/cord-272179-wvw5mmy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272179-wvw5mmy3.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-288167-976qxja2 author: Park, Wan Beom title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date: 2018-05-09 pages: extension: .txt txt: ./txt/cord-288167-976qxja2.txt cache: ./cache/cord-288167-976qxja2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288167-976qxja2.txt' === file2bib.sh === id: cord-257073-dm80bxnd author: Akmatov, Manas K. title: E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date: 2011-08-17 pages: extension: .txt txt: ./txt/cord-257073-dm80bxnd.txt cache: ./cache/cord-257073-dm80bxnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257073-dm80bxnd.txt' === file2bib.sh === id: cord-274845-pqvlh3eg author: Li, Yan title: Characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in Beijing date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-274845-pqvlh3eg.txt cache: ./cache/cord-274845-pqvlh3eg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274845-pqvlh3eg.txt' === file2bib.sh === id: cord-262017-utvy0i8l author: Tobar Vega, Pool title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-262017-utvy0i8l.txt cache: ./cache/cord-262017-utvy0i8l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262017-utvy0i8l.txt' === file2bib.sh === id: cord-258669-ubw6mdzi author: Colebunders, Robert title: A call for strengthened evidence on targeted, non-pharmaceutical interventions against COVID-19 for the protection of vulnerable individuals in sub-Saharan Africa date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-258669-ubw6mdzi.txt cache: ./cache/cord-258669-ubw6mdzi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258669-ubw6mdzi.txt' === file2bib.sh === id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-283590-xvnv17zy.txt cache: ./cache/cord-283590-xvnv17zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283590-xvnv17zy.txt' === file2bib.sh === id: cord-275866-m89hgf41 author: Li, Ping title: Clinical Features and Short-term Outcomes of Elderly Patients With COVID-19 date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-275866-m89hgf41.txt cache: ./cache/cord-275866-m89hgf41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275866-m89hgf41.txt' === file2bib.sh === id: cord-268037-szhzmzys author: Eshaghi, A. title: A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains date: 2008-12-17 pages: extension: .txt txt: ./txt/cord-268037-szhzmzys.txt cache: ./cache/cord-268037-szhzmzys.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268037-szhzmzys.txt' === file2bib.sh === id: cord-254872-w6d397js author: Stein, Richard A. title: Methicillin-resistant Staphylococcus aureus—the new zoonosis date: 2008-11-30 pages: extension: .txt txt: ./txt/cord-254872-w6d397js.txt cache: ./cache/cord-254872-w6d397js.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254872-w6d397js.txt' === file2bib.sh === id: cord-268883-nf4fm7r7 author: Corchuelo, Jairo title: Oral manifestations in a patient with a history of asymptomatic COVID-19. Case Report date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-268883-nf4fm7r7.txt cache: ./cache/cord-268883-nf4fm7r7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268883-nf4fm7r7.txt' === file2bib.sh === id: cord-262310-z0m6uuzf author: Effenberger, Maria title: Association of the COVID-19 pandemic with Internet Search Volumes: A Google TrendsTM Analysis date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-262310-z0m6uuzf.txt cache: ./cache/cord-262310-z0m6uuzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262310-z0m6uuzf.txt' === file2bib.sh === id: cord-275250-ilmgy7ce author: Xia, Yong title: Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-275250-ilmgy7ce.txt cache: ./cache/cord-275250-ilmgy7ce.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-275250-ilmgy7ce.txt' === file2bib.sh === id: cord-255021-acgfwjwi author: Luo, Ying title: Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-255021-acgfwjwi.txt cache: ./cache/cord-255021-acgfwjwi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255021-acgfwjwi.txt' === file2bib.sh === id: cord-305788-z75yv88e author: Agergaard, Charlotte Nielsen title: Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305788-z75yv88e.txt cache: ./cache/cord-305788-z75yv88e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305788-z75yv88e.txt' === file2bib.sh === id: cord-260332-tnz6k2z1 author: Tran, Tu Anh title: CT scan does not make a diagnosis of Covid-19: a cautionary case report() date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-260332-tnz6k2z1.txt cache: ./cache/cord-260332-tnz6k2z1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260332-tnz6k2z1.txt' === file2bib.sh === id: cord-276254-q04hqra2 author: Paul, Kishor Kumar title: Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-276254-q04hqra2.txt cache: ./cache/cord-276254-q04hqra2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276254-q04hqra2.txt' === file2bib.sh === id: cord-279581-d2l4nnex author: Abuhabib, A.A. title: Unique situation of Gaza Strip dealing with COVID-19 crisis date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-279581-d2l4nnex.txt cache: ./cache/cord-279581-d2l4nnex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279581-d2l4nnex.txt' === file2bib.sh === id: cord-282421-yialyuav author: Alcoba-Florez, Julia title: Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-282421-yialyuav.txt cache: ./cache/cord-282421-yialyuav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282421-yialyuav.txt' === file2bib.sh === id: cord-253102-z15j8izi author: Ross, Allen G.P. title: Planning for the Next Global Pandemic date: 2015-08-04 pages: extension: .txt txt: ./txt/cord-253102-z15j8izi.txt cache: ./cache/cord-253102-z15j8izi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253102-z15j8izi.txt' === file2bib.sh === id: cord-266253-oyid5haj author: Al-Abaidani, I.S. title: Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman date: 2014-10-29 pages: extension: .txt txt: ./txt/cord-266253-oyid5haj.txt cache: ./cache/cord-266253-oyid5haj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266253-oyid5haj.txt' === file2bib.sh === id: cord-274230-old0xmcc author: Zhao, Qianwen title: Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-274230-old0xmcc.txt cache: ./cache/cord-274230-old0xmcc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274230-old0xmcc.txt' === file2bib.sh === id: cord-254377-j8e8gb0l author: Ali, Sadaf title: Acute cor pulmonale from saddle pulmonary embolism in a patient with previous Covid-19 – should we prolong prophylactic anticoagulation? date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-254377-j8e8gb0l.txt cache: ./cache/cord-254377-j8e8gb0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254377-j8e8gb0l.txt' === file2bib.sh === id: cord-311479-8pjoz64q author: He, Daihai title: The relative transmissibility of asymptomatic cases among close contacts date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-311479-8pjoz64q.txt cache: ./cache/cord-311479-8pjoz64q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311479-8pjoz64q.txt' === file2bib.sh === id: cord-282360-byqhzyzi author: Zhang, Dingmei title: Enterovirus 71 vaccine: close but still far date: 2010-04-18 pages: extension: .txt txt: ./txt/cord-282360-byqhzyzi.txt cache: ./cache/cord-282360-byqhzyzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282360-byqhzyzi.txt' === file2bib.sh === id: cord-303417-1237ykxt author: d’Arminio Monforte, Antonella title: Effectiveness of Hydroxychloroquine in COVID-19 disease: A done and dusted situation? date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-303417-1237ykxt.txt cache: ./cache/cord-303417-1237ykxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303417-1237ykxt.txt' === file2bib.sh === id: cord-268389-0agwvsrv author: Kaminski, Monica A. title: Tocilizumab Therapy of COVID-19: A Comparison of Subcutaneous and Intravenous Therapies date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-268389-0agwvsrv.txt cache: ./cache/cord-268389-0agwvsrv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268389-0agwvsrv.txt' === file2bib.sh === id: cord-280627-dfnc9g2c author: Wang, Xiong title: Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-280627-dfnc9g2c.txt cache: ./cache/cord-280627-dfnc9g2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280627-dfnc9g2c.txt' === file2bib.sh === id: cord-008219-ng9xb46c author: Lassmann, Britta title: Highlights from the 6(th) International Meeting on Emerging Diseases and Surveillance (IMED 2016) Vienna, Austria from Nov 3 to 7, 2016 date: 2016-12-09 pages: extension: .txt txt: ./txt/cord-008219-ng9xb46c.txt cache: ./cache/cord-008219-ng9xb46c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008219-ng9xb46c.txt' === file2bib.sh === id: cord-278406-n5e3a09i author: Macauley, Precious title: CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-278406-n5e3a09i.txt cache: ./cache/cord-278406-n5e3a09i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278406-n5e3a09i.txt' === file2bib.sh === id: cord-255901-nl9k8uwd author: Barasheed, Osamah title: Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date: 2016-03-29 pages: extension: .txt txt: ./txt/cord-255901-nl9k8uwd.txt cache: ./cache/cord-255901-nl9k8uwd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255901-nl9k8uwd.txt' === file2bib.sh === id: cord-279976-juz9jnfk author: Xie, Mingxuan title: Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date: 2020-04-01 pages: extension: .txt txt: ./txt/cord-279976-juz9jnfk.txt cache: ./cache/cord-279976-juz9jnfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-279976-juz9jnfk.txt' === file2bib.sh === id: cord-297715-qcwp2jdv author: Machida, Masaki title: Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-297715-qcwp2jdv.txt cache: ./cache/cord-297715-qcwp2jdv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297715-qcwp2jdv.txt' === file2bib.sh === id: cord-308080-1heu9vuv author: Simulundu, Edgar title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-308080-1heu9vuv.txt cache: ./cache/cord-308080-1heu9vuv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308080-1heu9vuv.txt' === file2bib.sh === id: cord-283812-ocfjj79v author: Blumberg, Lucille title: Hosting of mass gathering sporting events during the 2013–2016 Ebola virus outbreak in West Africa: experience from three African countries date: 2016-06-15 pages: extension: .txt txt: ./txt/cord-283812-ocfjj79v.txt cache: ./cache/cord-283812-ocfjj79v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283812-ocfjj79v.txt' === file2bib.sh === id: cord-306682-01q775up author: Vijgen, Leen title: Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date: 2004-06-22 pages: extension: .txt txt: ./txt/cord-306682-01q775up.txt cache: ./cache/cord-306682-01q775up.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306682-01q775up.txt' === file2bib.sh === id: cord-261672-0cresfn8 author: Kim, Sungchan title: Evaluation of COVID-19 epidemic outbreak caused by temporal contact-increase in South Korea date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-261672-0cresfn8.txt cache: ./cache/cord-261672-0cresfn8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261672-0cresfn8.txt' === file2bib.sh === id: cord-274028-dvsvtsn0 author: Del Brutto, Oscar H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-274028-dvsvtsn0.txt cache: ./cache/cord-274028-dvsvtsn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274028-dvsvtsn0.txt' === file2bib.sh === id: cord-289304-9srk0ohb author: Bagnato, Sergio title: Critical illness myopathy after COVID-19 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-289304-9srk0ohb.txt cache: ./cache/cord-289304-9srk0ohb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289304-9srk0ohb.txt' === file2bib.sh === id: cord-257737-obadq502 author: Wu, Di title: Positive effects of COVID-19 control measures on influenza prevention date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-257737-obadq502.txt cache: ./cache/cord-257737-obadq502.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257737-obadq502.txt' === file2bib.sh === id: cord-259837-5tbdqzxr author: Kalcioglu, Mahmut Tayyar title: May COVID-19 cause sudden sensorineural hearing loss? date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-259837-5tbdqzxr.txt cache: ./cache/cord-259837-5tbdqzxr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259837-5tbdqzxr.txt' === file2bib.sh === id: cord-290100-wnjjqqn5 author: Wong, Samuel Y.S. title: Primary care physicians’ response to pandemic influenza in Hong Kong: a mixed quantitative and qualitative study date: 2012-07-11 pages: extension: .txt txt: ./txt/cord-290100-wnjjqqn5.txt cache: ./cache/cord-290100-wnjjqqn5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290100-wnjjqqn5.txt' === file2bib.sh === id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-258250-zueo1xfa.txt cache: ./cache/cord-258250-zueo1xfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258250-zueo1xfa.txt' === file2bib.sh === id: cord-301079-n1nytr6k author: Tan, Li title: Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-301079-n1nytr6k.txt cache: ./cache/cord-301079-n1nytr6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301079-n1nytr6k.txt' === file2bib.sh === id: cord-291638-oatrjbo3 author: Kang, Dayun title: Spatial epidemic dynamics of the COVID-19 outbreak in China date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-291638-oatrjbo3.txt cache: ./cache/cord-291638-oatrjbo3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291638-oatrjbo3.txt' === file2bib.sh === id: cord-265146-j0n3a4m6 author: Hsieh, Ying-Hen title: Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan date: 2013-02-12 pages: extension: .txt txt: ./txt/cord-265146-j0n3a4m6.txt cache: ./cache/cord-265146-j0n3a4m6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265146-j0n3a4m6.txt' === file2bib.sh === id: cord-292092-o6s5nw49 author: Furuse, Yuki title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date: 2015-09-30 pages: extension: .txt txt: ./txt/cord-292092-o6s5nw49.txt cache: ./cache/cord-292092-o6s5nw49.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292092-o6s5nw49.txt' === file2bib.sh === id: cord-287209-hkrarxsd author: Zhao, Shi title: The basic reproduction number of novel coronavirus (2019-nCoV) estimation based on exponential growth in the early outbreak in China from 2019 to 2020: A reply to Dhungana date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-287209-hkrarxsd.txt cache: ./cache/cord-287209-hkrarxsd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287209-hkrarxsd.txt' === file2bib.sh === id: cord-259501-iggw1exl author: Kim, Yong Yean title: Acute Respiratory Illness in Rural Haiti date: 2019-02-14 pages: extension: .txt txt: ./txt/cord-259501-iggw1exl.txt cache: ./cache/cord-259501-iggw1exl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-259501-iggw1exl.txt' === file2bib.sh === id: cord-257200-q0vqlerz author: Zumla, A. title: What is the experience from previous mass gathering events? Lessons for Zika virus and the Olympics 2016 date: 2016-06-15 pages: extension: .txt txt: ./txt/cord-257200-q0vqlerz.txt cache: ./cache/cord-257200-q0vqlerz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257200-q0vqlerz.txt' === file2bib.sh === id: cord-292988-q1yz9y8k author: Zumla, Alimuddin title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-292988-q1yz9y8k.txt cache: ./cache/cord-292988-q1yz9y8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292988-q1yz9y8k.txt' === file2bib.sh === id: cord-300583-0krbrj4w author: Koh, Wee Chian title: Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-300583-0krbrj4w.txt cache: ./cache/cord-300583-0krbrj4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300583-0krbrj4w.txt' === file2bib.sh === id: cord-304743-0bsdahh6 author: Kortepeter, Mark G title: Marburg Virus Disease: a Summary for Clinicians date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-304743-0bsdahh6.txt cache: ./cache/cord-304743-0bsdahh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304743-0bsdahh6.txt' === file2bib.sh === id: cord-311413-uiwjrvru author: Chanda-Kapata, Pascalina title: COVID-19 and malaria: A symptom screening challenge for malaria endemic countries date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-311413-uiwjrvru.txt cache: ./cache/cord-311413-uiwjrvru.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311413-uiwjrvru.txt' === file2bib.sh === id: cord-276445-m5vjo3ym author: Lee, Hyojung title: Recrudescence of Ebola virus disease outbreak in West Africa, 2014–2016 date: 2017-09-20 pages: extension: .txt txt: ./txt/cord-276445-m5vjo3ym.txt cache: ./cache/cord-276445-m5vjo3ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276445-m5vjo3ym.txt' === file2bib.sh === id: cord-297396-r1p7xn3a author: Ng, Ming-Yen title: Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-297396-r1p7xn3a.txt cache: ./cache/cord-297396-r1p7xn3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297396-r1p7xn3a.txt' === file2bib.sh === id: cord-268599-z54p3dk3 author: Panda, Swagatika title: Human metapneumovirus: review of an important respiratory pathogen date: 2014-05-17 pages: extension: .txt txt: ./txt/cord-268599-z54p3dk3.txt cache: ./cache/cord-268599-z54p3dk3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268599-z54p3dk3.txt' === file2bib.sh === id: cord-024631-yvek5vjz author: Althaus, T. title: Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-024631-yvek5vjz.txt cache: ./cache/cord-024631-yvek5vjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-024631-yvek5vjz.txt' === file2bib.sh === id: cord-261058-yu2qw02l author: Burgner, David title: Kawasaki disease: What is the epidemiology telling us about the etiology? date: 2005-06-03 pages: extension: .txt txt: ./txt/cord-261058-yu2qw02l.txt cache: ./cache/cord-261058-yu2qw02l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261058-yu2qw02l.txt' === file2bib.sh === id: cord-260518-mswb3q67 author: Zumla, Alimuddin title: Taking forward a ‘One Health’ approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential date: 2016-06-15 pages: extension: .txt txt: ./txt/cord-260518-mswb3q67.txt cache: ./cache/cord-260518-mswb3q67.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260518-mswb3q67.txt' === file2bib.sh === id: cord-290206-fmy4zrim author: Lim, Jue Tao title: The Costs of an Expanded Screening Criteria for COVID-19: A Modelling Study date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-290206-fmy4zrim.txt cache: ./cache/cord-290206-fmy4zrim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290206-fmy4zrim.txt' === file2bib.sh === id: cord-271495-5906wju4 author: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-271495-5906wju4.txt cache: ./cache/cord-271495-5906wju4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271495-5906wju4.txt' === file2bib.sh === id: cord-304872-hnxmtbrf author: Lv, Hao title: Prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with COVID‑19 in Wuhan, China date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-304872-hnxmtbrf.txt cache: ./cache/cord-304872-hnxmtbrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304872-hnxmtbrf.txt' === file2bib.sh === id: cord-305782-gnzwe2z2 author: Satici, Celal title: Performance of Pneumonia Severity Index and CURB-65 in Predicting 30-day mortality in patients with COVID-19 date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-305782-gnzwe2z2.txt cache: ./cache/cord-305782-gnzwe2z2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305782-gnzwe2z2.txt' === file2bib.sh === id: cord-310691-6danlh8h author: Ma, Simin title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-310691-6danlh8h.txt cache: ./cache/cord-310691-6danlh8h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310691-6danlh8h.txt' === file2bib.sh === id: cord-293630-zc8huo1j author: Capone, Alessandro title: Simultaneous circulation of COVID-19 and flu in Italy: potential combined effects on the risk of death? date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-293630-zc8huo1j.txt cache: ./cache/cord-293630-zc8huo1j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293630-zc8huo1j.txt' === file2bib.sh === id: cord-293247-ltxt2dfv author: Elachola, Habida title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings date: 2015-10-09 pages: extension: .txt txt: ./txt/cord-293247-ltxt2dfv.txt cache: ./cache/cord-293247-ltxt2dfv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293247-ltxt2dfv.txt' === file2bib.sh === id: cord-277640-vy7ex5lv author: Calderaro, Adriana title: SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-277640-vy7ex5lv.txt cache: ./cache/cord-277640-vy7ex5lv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277640-vy7ex5lv.txt' === file2bib.sh === id: cord-308114-68cgub5o author: Afrin, Lawrence B. title: Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-308114-68cgub5o.txt cache: ./cache/cord-308114-68cgub5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308114-68cgub5o.txt' === file2bib.sh === id: cord-275191-lgze4zex author: Al-Sadeq, Duaa W. title: The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-275191-lgze4zex.txt cache: ./cache/cord-275191-lgze4zex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275191-lgze4zex.txt' === file2bib.sh === id: cord-293942-n5ypkftc author: Takoi, Hiroyuki title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-293942-n5ypkftc.txt cache: ./cache/cord-293942-n5ypkftc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293942-n5ypkftc.txt' === file2bib.sh === id: cord-280060-gzby85u9 author: Rello, Jordi title: Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() date: 2016-04-28 pages: extension: .txt txt: ./txt/cord-280060-gzby85u9.txt cache: ./cache/cord-280060-gzby85u9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280060-gzby85u9.txt' === file2bib.sh === id: cord-273961-ja8xggnd author: Nakagawara, Kensuke title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date: 2020-07-26 pages: extension: .txt txt: ./txt/cord-273961-ja8xggnd.txt cache: ./cache/cord-273961-ja8xggnd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273961-ja8xggnd.txt' === file2bib.sh === id: cord-292256-jp80u828 author: Moriguchi, Takeshi title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-292256-jp80u828.txt cache: ./cache/cord-292256-jp80u828.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292256-jp80u828.txt' === file2bib.sh === id: cord-315059-l6guql8q author: Mubarak, Naeem title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. Time for some unpopular decisions date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-315059-l6guql8q.txt cache: ./cache/cord-315059-l6guql8q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-315059-l6guql8q.txt' === file2bib.sh === id: cord-291367-rtmsrh16 author: Zumla, Alimuddin title: Middle East Respiratory Syndrome - need for increased vigilance and watchful surveillance for MERS-CoV in sub-Saharan Africa date: 2015-07-02 pages: extension: .txt txt: ./txt/cord-291367-rtmsrh16.txt cache: ./cache/cord-291367-rtmsrh16.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291367-rtmsrh16.txt' === file2bib.sh === id: cord-311453-l6quzef6 author: Klopfenstein, Timothée title: Impact of Tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 COVID-19 patients date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-311453-l6quzef6.txt cache: ./cache/cord-311453-l6quzef6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311453-l6quzef6.txt' === file2bib.sh === id: cord-301085-tk2vvxj7 author: Askarian, Mehrdad title: Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran date: 2006-07-11 pages: extension: .txt txt: ./txt/cord-301085-tk2vvxj7.txt cache: ./cache/cord-301085-tk2vvxj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301085-tk2vvxj7.txt' === file2bib.sh === id: cord-273090-fdzkfo1u author: He, Susu title: Relationship between Chest CT manifestations and immune response in COVID-19 patients date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-273090-fdzkfo1u.txt cache: ./cache/cord-273090-fdzkfo1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273090-fdzkfo1u.txt' === file2bib.sh === id: cord-279892-37vyazby author: Sun, Guanghao title: Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases date: 2017-01-16 pages: extension: .txt txt: ./txt/cord-279892-37vyazby.txt cache: ./cache/cord-279892-37vyazby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279892-37vyazby.txt' === file2bib.sh === id: cord-311026-mpr3xb2a author: Petersen, Eskild title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-311026-mpr3xb2a.txt cache: ./cache/cord-311026-mpr3xb2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311026-mpr3xb2a.txt' === file2bib.sh === id: cord-257265-lkzytud0 author: Zheng, Fang title: SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-257265-lkzytud0.txt cache: ./cache/cord-257265-lkzytud0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257265-lkzytud0.txt' === file2bib.sh === id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-302409-40ktyt5q.txt cache: ./cache/cord-302409-40ktyt5q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302409-40ktyt5q.txt' === file2bib.sh === id: cord-283891-m36un1y2 author: Hu, Bisong title: First, second and potential third generation spreads of the COVID-19 epidemic in mainland China: an early exploratory study incorporating location-based service data of mobile devices date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-283891-m36un1y2.txt cache: ./cache/cord-283891-m36un1y2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283891-m36un1y2.txt' === file2bib.sh === id: cord-309032-idjdzs97 author: Zhou, Feng title: Epidemiological Characteristics and Factors Associated with Critical Time Intervals of COVID-19 in Eighteen Provinces, China: A Retrospective Study date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-309032-idjdzs97.txt cache: ./cache/cord-309032-idjdzs97.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309032-idjdzs97.txt' === file2bib.sh === id: cord-286743-z0e5arlm author: Langer-Gould, Annette title: Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-286743-z0e5arlm.txt cache: ./cache/cord-286743-z0e5arlm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286743-z0e5arlm.txt' === file2bib.sh === id: cord-300774-5mrkmctl author: Hernández-Mora, Miguel Górgolas title: Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-300774-5mrkmctl.txt cache: ./cache/cord-300774-5mrkmctl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300774-5mrkmctl.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 66886 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67264 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 66989 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-317500-ufo2qgj4 author: Scialpi, Michele title: Pulmonary thromboembolism in criticall ill COVID-19 patients date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-317500-ufo2qgj4.txt cache: ./cache/cord-317500-ufo2qgj4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317500-ufo2qgj4.txt' === file2bib.sh === id: cord-305763-160heazx author: Lai, Chih-Cheng title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-305763-160heazx.txt cache: ./cache/cord-305763-160heazx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305763-160heazx.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67961 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68003 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67723 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68170 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67953 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67985 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-317080-kn56oov6 author: Quadri, Sayed. A. title: COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-317080-kn56oov6.txt cache: ./cache/cord-317080-kn56oov6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317080-kn56oov6.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67928 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68457 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68007 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67979 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68163 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-311654-ixn65hxb author: Zumla, Alimuddin title: COVID-19 and the scaled-down 2020 Hajj Pilgrimage - Decisive, logical and prudent decision making by Saudi authorities overcomes pre-Hajj public health concerns date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-311654-ixn65hxb.txt cache: ./cache/cord-311654-ixn65hxb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311654-ixn65hxb.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68016 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68017 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-317399-693q80xo author: Al Wahaibi, Adil title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-317399-693q80xo.txt cache: ./cache/cord-317399-693q80xo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-317399-693q80xo.txt' === file2bib.sh === id: cord-320785-42p8292o author: Lobo, Andréa de Paula title: COVID-19 epidemic in Brazil: where we at? date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-320785-42p8292o.txt cache: ./cache/cord-320785-42p8292o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320785-42p8292o.txt' === file2bib.sh === id: cord-340279-bq5owwot author: Espíndola, Otávio de Melo title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-340279-bq5owwot.txt cache: ./cache/cord-340279-bq5owwot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340279-bq5owwot.txt' === file2bib.sh === id: cord-339576-0d6sa9pe author: Guallar, María Pilar title: Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-339576-0d6sa9pe.txt cache: ./cache/cord-339576-0d6sa9pe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339576-0d6sa9pe.txt' === file2bib.sh === id: cord-338225-8dlxnpcn author: De Meyer, Sandra title: Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-338225-8dlxnpcn.txt cache: ./cache/cord-338225-8dlxnpcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338225-8dlxnpcn.txt' === file2bib.sh === id: cord-328459-nmd81sue author: Dioscoridi, Lorenzo title: Covid-19 exposure risk for family members of healthcare workers: an observational study date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-328459-nmd81sue.txt cache: ./cache/cord-328459-nmd81sue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328459-nmd81sue.txt' === file2bib.sh === id: cord-338576-gh1plurq author: Regen, Francesca title: A Simple Approach to Optimum Pool Size for Pooled SARS-CoV-2 Testing date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-338576-gh1plurq.txt cache: ./cache/cord-338576-gh1plurq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338576-gh1plurq.txt' === file2bib.sh === id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-334603-yt2pmxi3.txt cache: ./cache/cord-334603-yt2pmxi3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334603-yt2pmxi3.txt' === file2bib.sh === id: cord-316209-juvmabdq author: Rutayisire, Erigene title: What works and what does not work in response to COVID-19 prevention and control in Africa date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-316209-juvmabdq.txt cache: ./cache/cord-316209-juvmabdq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316209-juvmabdq.txt' === file2bib.sh === id: cord-318808-1cfwj5uq author: Li, Ying title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-318808-1cfwj5uq.txt cache: ./cache/cord-318808-1cfwj5uq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318808-1cfwj5uq.txt' === file2bib.sh === id: cord-284652-7npya3yx author: Shim, Eunha title: Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020 date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-284652-7npya3yx.txt cache: ./cache/cord-284652-7npya3yx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284652-7npya3yx.txt' === file2bib.sh === id: cord-326143-6ndqgxy8 author: Wang, Qiang title: Successful recovery of severe COVID-19 with cytokine storm treating with extracorporeal blood purification date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-326143-6ndqgxy8.txt cache: ./cache/cord-326143-6ndqgxy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326143-6ndqgxy8.txt' === file2bib.sh === id: cord-320902-1hfxju5f author: Filocamo, Giovanni title: Use of anakinra in severe COVID-19: a case report date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-320902-1hfxju5f.txt cache: ./cache/cord-320902-1hfxju5f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320902-1hfxju5f.txt' === file2bib.sh === id: cord-320829-uepneyug author: He, Zhongping title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 pages: extension: .txt txt: ./txt/cord-320829-uepneyug.txt cache: ./cache/cord-320829-uepneyug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320829-uepneyug.txt' === file2bib.sh === id: cord-330136-o8df8szx author: Fan, Hua title: Cardiac injuries in patients with coronavirus disease 2019: Not to be ignored date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-330136-o8df8szx.txt cache: ./cache/cord-330136-o8df8szx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330136-o8df8szx.txt' === file2bib.sh === id: cord-323696-0lq8ql6n author: Bearman, Gonzalo title: Reflections on the COVID-19 Pandemic in the USA: Will We Better Prepared Next Time? date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-323696-0lq8ql6n.txt cache: ./cache/cord-323696-0lq8ql6n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323696-0lq8ql6n.txt' === file2bib.sh === id: cord-320860-qt84oicg author: Zhang, Aining title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-320860-qt84oicg.txt cache: ./cache/cord-320860-qt84oicg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320860-qt84oicg.txt' === file2bib.sh === id: cord-318315-r6wqywwe author: Memish, Ziad A. title: Etiology of severe community-acquired pneumonia during the 2013 Hajj—part of the MERS-CoV surveillance program date: 2014-06-23 pages: extension: .txt txt: ./txt/cord-318315-r6wqywwe.txt cache: ./cache/cord-318315-r6wqywwe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318315-r6wqywwe.txt' === file2bib.sh === id: cord-324231-nik7xizn author: Aitsi-Selmi, Amina title: Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction date: 2016-04-07 pages: extension: .txt txt: ./txt/cord-324231-nik7xizn.txt cache: ./cache/cord-324231-nik7xizn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324231-nik7xizn.txt' === file2bib.sh === id: cord-326881-3j2e92dj author: Vassallo, M. title: Patients with Covid-19 exhibit different immunological profiles according to their clinical presentation date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-326881-3j2e92dj.txt cache: ./cache/cord-326881-3j2e92dj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326881-3j2e92dj.txt' === file2bib.sh === id: cord-319814-tyqb473m author: Zhang, Dingmei title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 pages: extension: .txt txt: ./txt/cord-319814-tyqb473m.txt cache: ./cache/cord-319814-tyqb473m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319814-tyqb473m.txt' === file2bib.sh === id: cord-315860-9j667c03 author: Jullien, Sophie title: Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-315860-9j667c03.txt cache: ./cache/cord-315860-9j667c03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315860-9j667c03.txt' === file2bib.sh === id: cord-317910-rwhwo55z author: Aziz, Asma B. title: Integrated control of COVID-19 in resource poor countries date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-317910-rwhwo55z.txt cache: ./cache/cord-317910-rwhwo55z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317910-rwhwo55z.txt' === file2bib.sh === id: cord-317624-qdzhncs0 author: Choi, Min Joo title: Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-317624-qdzhncs0.txt cache: ./cache/cord-317624-qdzhncs0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317624-qdzhncs0.txt' === file2bib.sh === id: cord-316505-tdlj5smv author: Kumar, Abhai title: Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers date: 2013-11-28 pages: extension: .txt txt: ./txt/cord-316505-tdlj5smv.txt cache: ./cache/cord-316505-tdlj5smv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316505-tdlj5smv.txt' === file2bib.sh === id: cord-336954-rh88lod0 author: Shim, Eunha title: Transmission potential and severity of COVID-19 in South Korea date: 2020-03-18 pages: extension: .txt txt: ./txt/cord-336954-rh88lod0.txt cache: ./cache/cord-336954-rh88lod0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336954-rh88lod0.txt' === file2bib.sh === id: cord-344478-5gp7v1uh author: Rosenberg, Eli S. title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-344478-5gp7v1uh.txt cache: ./cache/cord-344478-5gp7v1uh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344478-5gp7v1uh.txt' === file2bib.sh === id: cord-341775-mucatzaa author: Shafi, Shuja title: The annual Hajj pilgrimage—minimizing the risk of ill health in pilgrims from Europe and opportunity for driving the best prevention and health promotion guidelines date: 2016-06-22 pages: extension: .txt txt: ./txt/cord-341775-mucatzaa.txt cache: ./cache/cord-341775-mucatzaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341775-mucatzaa.txt' === file2bib.sh === id: cord-318181-xxc7vdnt author: Ahmed, Anwar E. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 pages: extension: .txt txt: ./txt/cord-318181-xxc7vdnt.txt cache: ./cache/cord-318181-xxc7vdnt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318181-xxc7vdnt.txt' === file2bib.sh === id: cord-323455-26xi2lqf author: AlBarrak, Ali title: Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date: 2018-02-21 pages: extension: .txt txt: ./txt/cord-323455-26xi2lqf.txt cache: ./cache/cord-323455-26xi2lqf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323455-26xi2lqf.txt' === file2bib.sh === id: cord-332348-yi85sfks author: Liang, Yujie title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-332348-yi85sfks.txt cache: ./cache/cord-332348-yi85sfks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332348-yi85sfks.txt' === file2bib.sh === id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-324295-9c1zxjng.txt cache: ./cache/cord-324295-9c1zxjng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324295-9c1zxjng.txt' === file2bib.sh === id: cord-325325-xw7627x9 author: Skeik, Nedaa title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 pages: extension: .txt txt: ./txt/cord-325325-xw7627x9.txt cache: ./cache/cord-325325-xw7627x9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325325-xw7627x9.txt' === file2bib.sh === id: cord-340992-88t1c0zs author: Nikolai, Lea A title: Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-340992-88t1c0zs.txt cache: ./cache/cord-340992-88t1c0zs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340992-88t1c0zs.txt' === file2bib.sh === id: cord-330819-vfagxsdz author: Althouse, Benjamin M title: Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date: 2018-08-14 pages: extension: .txt txt: ./txt/cord-330819-vfagxsdz.txt cache: ./cache/cord-330819-vfagxsdz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330819-vfagxsdz.txt' === file2bib.sh === id: cord-345275-h0hvaxgx author: Sun, Mengyao title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-345275-h0hvaxgx.txt cache: ./cache/cord-345275-h0hvaxgx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345275-h0hvaxgx.txt' Que is empty; done journal-intJInfectDis-cord === reduce.pl bib === id = cord-257073-dm80bxnd author = Akmatov, Manas K. title = E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date = 2011-08-17 pages = extension = .txt mime = text/plain words = 3515 sentences = 177 flesch = 46 summary = OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. cache = ./cache/cord-257073-dm80bxnd.txt txt = ./txt/cord-257073-dm80bxnd.txt === reduce.pl bib === id = cord-255901-nl9k8uwd author = Barasheed, Osamah title = Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date = 2016-03-29 pages = extension = .txt mime = text/plain words = 4522 sentences = 256 flesch = 50 summary = Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. cache = ./cache/cord-255901-nl9k8uwd.txt txt = ./txt/cord-255901-nl9k8uwd.txt === reduce.pl bib === id = cord-268389-0agwvsrv author = Kaminski, Monica A. title = Tocilizumab Therapy of COVID-19: A Comparison of Subcutaneous and Intravenous Therapies date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3409 sentences = 184 flesch = 47 summary = This study aimed to compare the effects of intravenous (IV) and subcutaneous (SC) tocilizumab, an IL-6 receptor antagonist, on respiratory parameters and clinical outcome in patients with COVID 19. C-reactive protein levels were significantly higher in patients in the IV group that did not respond (Table 2) Lastly, laboratory markers of inflammation were analyzed before and during the seven days following tocilizumab therapy to identify trends that correlated with response involving the respiratory parameters (Table 3) . Tocilizumab has been found to be associated with improved outcomes in patients with COVID-19 related respiratory disease, particularly for patients with critical illness (i.e., requiring mechanical ventilation) (Rossotti et al., 2020 , Somers et al., 2020 . In our report, levels of C-reactive protein fell acutely in both patients that did and did not have improvement in respiratory parameters seven days following tocilizumab therapy. cache = ./cache/cord-268389-0agwvsrv.txt txt = ./txt/cord-268389-0agwvsrv.txt === reduce.pl bib === id = cord-258669-ubw6mdzi author = Colebunders, Robert title = A call for strengthened evidence on targeted, non-pharmaceutical interventions against COVID-19 for the protection of vulnerable individuals in sub-Saharan Africa date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2516 sentences = 120 flesch = 48 summary = We suggest investigating the feasibility, acceptability, and efficacy of distributing COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. Here, we call for the generation and strengthening of evidence to guide non-pharmaceutical interventions for COVID-19, which we illustrate with a practical proposal for assessing the impact of targeted protection of at-risk individuals in settings in sub-Saharan Africa. Although the early implementation of lockdown measures for COVID-19 control may have contributed to the (initially) low mortality observed in most sub-Saharan Africa countries, the collateral damage resulting from this strategy is becoming increasingly apparent. We therefore propose to complement the extant containment measures in sub-Saharan Africa with more targeted protection strategies, aiming at protecting people at risk of severe COVID-19 disease. One strategy could be to distribute COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. cache = ./cache/cord-258669-ubw6mdzi.txt txt = ./txt/cord-258669-ubw6mdzi.txt === reduce.pl bib === id = cord-274845-pqvlh3eg author = Li, Yan title = Characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in Beijing date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1341 sentences = 76 flesch = 56 summary = Here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory virus infection. COVID-19 group (83.33%) had higher rate of pneumonia in chest CT scan than Flu A and B virus infection groups. There was no statistical difference in complete blood count parameters between Similar to what was reported in COVID-19 [9] , fever was the most common symptom in the respiratory virus infection patients. In this study, the ratio of fever and the highest temperature were higher in Flu A virus infection patients than in COVID-19 patients. And in this study, it showed that COVID-19 patients even had lower WBC count and neutrophil count than Flu A virus and RSV infection group. Also, it was reported that they had low lymphocyte count [9, 10] , but this study found that the lymphocyte count was higher in COVID-19 than in Flu A and B virus infection patients. cache = ./cache/cord-274845-pqvlh3eg.txt txt = ./txt/cord-274845-pqvlh3eg.txt === reduce.pl bib === id = cord-029882-kufs0fxe author = Malviya, Amit title = The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials date = 2020-07-29 pages = extension = .txt mime = text/plain words = 483 sentences = 34 flesch = 57 summary = HCQ is touted for treatment of Covid 19 primarily based on its anti-viral properties, thus the timing of administration becomes very important for a meaning full assessment of study results. Recently it been shown that this score is not accurate for predicting severity of disease in Covid 19 patients . Covid 19 is a multisystem disease and the disease itself promotes proarrhythmic milieu with prolonged QT intervals at baseline .5,6 Risk assessment of HCQ therapy is not complete if such patients are excluded. Finally , mechanism of action of HCQ against is a part of its broad anti-viral and immunomodulatory properties and no specific pharmacologic actions are described for SARS-CoV-2 infection. 9,10 Weather HCQ as initial anti-viral agent prevents progression to severe disease is not known clearly . Ventricular arrhythmia risk due to chloroquine / hydroxychloroquine treatment for COVID-19: Should it be given Effects of chloroquine on viral infections: an old drug against today's diseases? cache = ./cache/cord-029882-kufs0fxe.txt txt = ./txt/cord-029882-kufs0fxe.txt === reduce.pl bib === id = cord-258881-74aijckl author = Wang, Maomao title = Case Report: One Case of Coronavirus Desease 2019(COVID-19) in Patient Co-nfected by HIV With a Low CD4+ T Cell Count date = 2020-04-23 pages = extension = .txt mime = text/plain words = 670 sentences = 45 flesch = 64 summary = Abstract The ongoing outbreak of COVID-19 that began in Wuhan, China has become an emergency of international concern When thousands of peolple were infected around the world.We report a case infected by SARS-Cov-2 and HIV simultaneously,which showed a longer course of disease and slower generation of specific antibody. Here we report a patient infected by SARS-Cov-2 , who had a relatively long course of disease with unstable state. Then eight markers of infectious diseases was checked and the result showed that abtibodies to HIV and syphilis were positive .Then the patient was transferred to specialty hospital for further treatment on March 8. People are generally susceptible to SARS-Cov-2 infection, especially the elderly patients and those with underlying diseases [2] . The author suggested that SARS-Cov-2 might damage lymphocytes, especially T lymphocytes, and the immune system was impaired during the period of disease [2] . In conclusion, we report the clinical features of a patient infected by SARS-Cov-2 and HIV. cache = ./cache/cord-258881-74aijckl.txt txt = ./txt/cord-258881-74aijckl.txt === reduce.pl bib === id = cord-262017-utvy0i8l author = Tobar Vega, Pool title = Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date = 2019-06-21 pages = extension = .txt mime = text/plain words = 1526 sentences = 92 flesch = 40 summary = title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. Endemic to Southeast Asia, East Asia and China, Talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (Supparatpinyo et al., 1994) . In the U.S. patients with HIV infection usually undergo testing for endemic fungal infections such as Blastomyces, Histoplasma, Coccidioides and Paracoccidioides. To our knowledge, this is the first case reporting systemic mycosis due toTalaromyces marneffei with associated hyponatremia secondary to SIADH and cross-reactivity with Blastomyces and Histoplasma in urine antigen testing. cache = ./cache/cord-262017-utvy0i8l.txt txt = ./txt/cord-262017-utvy0i8l.txt === reduce.pl bib === id = cord-282360-byqhzyzi author = Zhang, Dingmei title = Enterovirus 71 vaccine: close but still far date = 2010-04-18 pages = extension = .txt mime = text/plain words = 4404 sentences = 248 flesch = 43 summary = To overcome the potential problem of reversion to virulence of attenuated strain vaccine, subunit vaccines consisting of only one or a few 'subunit' proteins of the pathogen that can stimulate immune responses directed at the intact virus have been developed using recombinant DNA technology. 21 have described a recombinant VP1 protein expressed in Escherichia coli BL21, showing that the VP1 protein with a complete adjuvant is able to elicit a neutralizing antibody response, enhance T helper cell proliferation, and induce high levels of interleukin (IL)-10 and interferon (IFN)-g in mice, providing direct evidence that the VP1 protein contains neutralizing epitopes independent of other viral capsid proteins; this paves the way for the use of VP1 as a backbone antigen for developing subunit vaccines against EV71. Protection against lethal enterovirus 71 infection in newborn mice by passive immunization with subunit VP1 vaccines and inactivated virus cache = ./cache/cord-282360-byqhzyzi.txt txt = ./txt/cord-282360-byqhzyzi.txt === reduce.pl bib === id = cord-283590-xvnv17zy author = Chen, Dabiao title = Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date = 2020-03-05 pages = extension = .txt mime = text/plain words = 1499 sentences = 96 flesch = 48 summary = Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People's Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). cache = ./cache/cord-283590-xvnv17zy.txt txt = ./txt/cord-283590-xvnv17zy.txt === reduce.pl bib === id = cord-262310-z0m6uuzf author = Effenberger, Maria title = Association of the COVID-19 pandemic with Internet Search Volumes: A Google TrendsTM Analysis date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2774 sentences = 145 flesch = 59 summary = Methods We performed a Google TrendsTM search for "Coronavirus" and compared Relative Search Volumes (RSV) indices to the number of reported COVID-19 cases by the European Center for Disease Control (ECDC) using time-lag correlation analysis. The worldwide Google TrendsTM index reached its peak on the 12th of March 2020 at a time when numbers of infected patients started to increase in Europe and COVID-19 was declared a pandemic. In European countries, especially in Italy, a small peak in the Google Trends TM analysis was found during the outbreak in China and a climax was found on February 23 rd 2020, a few days before the numbers of newly COVID-19 started to increase exponentially. The peak of search queries was March 3 rd a new increase in RSV is found in Brazil, followed by increasing numbers of newly confirmed cases of COVID-19 ( Figure 2 ). cache = ./cache/cord-262310-z0m6uuzf.txt txt = ./txt/cord-262310-z0m6uuzf.txt === reduce.pl bib === id = cord-259501-iggw1exl author = Kim, Yong Yean title = Acute Respiratory Illness in Rural Haiti date = 2019-02-14 pages = extension = .txt mime = text/plain words = 4623 sentences = 227 flesch = 54 summary = Earlier studies in resource-poor settings have identified Streptococcus pneumoniae, Haemophilus influenzae type B and Staphylococcus aureus as important bacterial causes of ARI, and respiratory syncytial virus (RSV) and Influenza as important viral causes (Rudan et al., 2008) . A multicountry study that included Haiti showed that agents detected in hospitalized children less than 5 years of age who had pneumonia included RSV, Influenza A and B, Parainfluenza viruses, Adenovirus and Human metapneumovirus (HMPV) (Bénet et al., 2017) . Analysis of specific viral or bacterial agents detected showed more children with FluA or FluB had LRTI (33%) compared to URTI (15%) [ Table 5 ]. The overall findings of RV as the most common virus detected followed by Influenza in Haiti is comparable to that found in studies of children in other tropical, resource-poor countries (Hoffman et al., 2012; Schlaudecker et al., 2012; Taylor et al., 2017) . cache = ./cache/cord-259501-iggw1exl.txt txt = ./txt/cord-259501-iggw1exl.txt === reduce.pl bib === id = cord-272015-1anph6qi author = Dauby, Nicolas title = The unfinished story of hydroxychloroquine in COVID-19: the right anti-inflammatory dose at the right moment? date = 2020-10-17 pages = extension = .txt mime = text/plain words = 959 sentences = 65 flesch = 43 summary = The observation by Lammers et al (Lammers et al.) that early HCQ treatment after admission at low dosage (2400 mg in total) is associated with lower risk of admission in intensive care unit coincides with large observational studies showing a lower mortality rate in patients exposed to HCQ therapy compared to no or other treatment. Another recent large cohort study of patients on low-dose HCQ for inflammatory disorders reported an association between chronic HCQ use and reduced mortality following SARS-CoV-2 infection (Gentry et al. The association of treatment with hydroxychloroquine and hospital mortality in COVID-19 patients Low-dose hydroxychloroquine therapy and mortality in hospitalised patients with COVID-19: a nationwide observational study of 8075 participants Use of hydroxychloroquine in hospitalised COVID-19 patients is associated with reduced mortality: Findings from the observational multicentre Italian CORIST study Longterm hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study cache = ./cache/cord-272015-1anph6qi.txt txt = ./txt/cord-272015-1anph6qi.txt === reduce.pl bib === id = cord-258078-k7y8k1vx author = Jang, Sukbin title = Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1475 sentences = 92 flesch = 50 summary = title: Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy We report three cases of COVID-19 pneumonia who progressed while using antiviral drugs and needed supplementary oxygen therapy, improved after treatment with nafamostat. Three COVID-19 patients had the following conditions: pneumonia with progression despite antiviral treatment; were elderly, over 65 years; and had underlying diseases that were known as high risk J o u r n a l P r e -p r o o f factors. On admission, he was not dyspneic or cyanotic, with a body temperature of 37.0°C, respiratory rate of 20 breaths per minute, heart rate of 75 beats per minute, and blood pressure of 140/90 mmHg. Initial laboratory results were as follows: white blood cell (WBC) count 5,150/μL (65% segmented neutrophil), and C-reactive protein (CRP) 2.61 mg/dL. cache = ./cache/cord-258078-k7y8k1vx.txt txt = ./txt/cord-258078-k7y8k1vx.txt === reduce.pl bib === id = cord-272179-wvw5mmy3 author = Calderaro, Adriana title = Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date = 2020-10-02 pages = extension = .txt mime = text/plain words = 1095 sentences = 70 flesch = 53 summary = title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children cache = ./cache/cord-272179-wvw5mmy3.txt txt = ./txt/cord-272179-wvw5mmy3.txt === reduce.pl bib === id = cord-275866-m89hgf41 author = Li, Ping title = Clinical Features and Short-term Outcomes of Elderly Patients With COVID-19 date = 2020-05-31 pages = extension = .txt mime = text/plain words = 2359 sentences = 145 flesch = 55 summary = Methods 204 elderly patients (≥60 years old) diagnosed with COVID-19 in Renmin Hospital of Wuhan University from January 31st to February 20th, 2020 were included in this study. Multivariate analysis showed that dyspnea (hazards ratio (HR) 2.2, 95% confidence interval (CI) 1.414 to 3.517;p < 0.001), older age (HR 1.1, 95% CI 1.070 to 1.123; p < 0.001), neutrophilia (HR 4.4, 95% CI 1.310 to 15.061; p = 0.017) and elevated ultrasensitive cardiac troponin I (HR 3.9, 95% CI 1.471 to 10.433; p = 0.006) were independently associated with death. Univariate analysis showed age of 70 years or older, comorbidity (hypertension, J o u r n a l P r e -p r o o f cardiovascular disease, COPD, chronic renal failure), onset of dyspnea, and several laboratory indices abnormalities were associated with poor outcome. This study suggests that the elderly patients of COVID-19 have a rapid course of the disease and a higher case fatality ratio. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China cache = ./cache/cord-275866-m89hgf41.txt txt = ./txt/cord-275866-m89hgf41.txt === reduce.pl bib === id = cord-276254-q04hqra2 author = Paul, Kishor Kumar title = Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh date = 2020-06-02 pages = extension = .txt mime = text/plain words = 3829 sentences = 202 flesch = 50 summary = title: Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh In this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. (Khatun et al., 2015 , Salje et al., 2016b Here we use the results from a detailed investigation of an outbreak of chikungunya virus in a village in Tangail, Bangladesh where the outbreak team visited every household in the community and interviewed all members in each household. This investigation suggests that chikungunya virus has become an emerging public health problem in Bangladesh, and outbreak investigations of emerging infections often have the objective of estimating attack rates of diseases and identifying the risk factors that lead to infection. cache = ./cache/cord-276254-q04hqra2.txt txt = ./txt/cord-276254-q04hqra2.txt === reduce.pl bib === id = cord-282177-8l7zukg4 author = Lin, Yi-Chun title = A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date = 2020-05-26 pages = extension = .txt mime = text/plain words = 370 sentences = 31 flesch = 55 summary = title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 cache = ./cache/cord-282177-8l7zukg4.txt txt = ./txt/cord-282177-8l7zukg4.txt === reduce.pl bib === id = cord-268037-szhzmzys author = Eshaghi, A. title = A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains date = 2008-12-17 pages = extension = .txt mime = text/plain words = 806 sentences = 54 flesch = 46 summary = authors: Eshaghi, A.; Blair, J.; Burton, L.; Lombos, E.; Choi, K.; De Lima, C.; Drews, S.J. title: A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains The purpose of this brief investigation was to determine whether nasopharyngeal specimens from patients infected with strains of influenza A (H1N1) carrying the H274Y mutation were more likely than not to contain other commonly circulating respiratory viral pathogens. Isolate sequences were compared to sequences with described H274Y mutations: GenBank accession No. 7 Specimens corresponding to H274Y mutant and H274 wild-type isolates were blinded and chosen at random for a retrospective investigation for other respiratory viral pathogens (adenovirus, coronavirus 229E/NL63, coronavirus OC43, influenza A/B, parainfluenza virus 1/2/3, respiratory syncytial virus A/B, rhinovirus A) using the Seeplex 1 RV detection kit protocol (Seegene, Inc., Rockville, MD). cache = ./cache/cord-268037-szhzmzys.txt txt = ./txt/cord-268037-szhzmzys.txt === reduce.pl bib === id = cord-254872-w6d397js author = Stein, Richard A. title = Methicillin-resistant Staphylococcus aureus—the new zoonosis date = 2008-11-30 pages = extension = .txt mime = text/plain words = 1670 sentences = 90 flesch = 36 summary = The surge in community-associated MRSA, at a time when reports of animal-to-human transmission are increasing, might not be merely coincidental, 12, 13 and according to a recent study conducted in the Netherlands, MRSA that entered from an animal reservoir into the human population is now responsible for over 20% of the strains isolated. 14 Findings that have accumulated in recent years make it necessary to define three additional patient groups at high risk for zoonotic MRSA: individuals in contact with farm animals, contacts of household pets, and veterinarian staff. Moreover, it is important to note that MRSA strains of animal origin have been isolated from people lacking previous documented direct animal contacts, supporting the possibility that direct human-to-human transmission occurs subsequent to one person's colonization/infection. Methicillin (oxacillin)-resistant Staphylococcus aureus strains isolated from major food animals and their potential transmission to humans An outbreak of methicillin-resistant Staphylococcus aureus skin infections resulting from horse to human transmission in a veterinary hospital cache = ./cache/cord-254872-w6d397js.txt txt = ./txt/cord-254872-w6d397js.txt === reduce.pl bib === id = cord-268599-z54p3dk3 author = Panda, Swagatika title = Human metapneumovirus: review of an important respiratory pathogen date = 2014-05-17 pages = extension = .txt mime = text/plain words = 5570 sentences = 308 flesch = 39 summary = Human metapneumovirus (hMPV), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immune-compromised patients. Human metapneumovirus (hMPV), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immunecompromised patients. hMPV is the major etiological agent responsible for about 5% to 10% of hospitalizations of children suffering from acute respiratory tract infections. hMPV infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. hMPV infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. Detection of human metapneumovirus in hospitalized children with acute respiratory tract infection using real-time RT-PCR in a hospital in northern Taiwan Human metapneumovirus infection in young children hospitalized with respiratory tract disease cache = ./cache/cord-268599-z54p3dk3.txt txt = ./txt/cord-268599-z54p3dk3.txt === reduce.pl bib === id = cord-257200-q0vqlerz author = Zumla, A. title = What is the experience from previous mass gathering events? Lessons for Zika virus and the Olympics 2016 date = 2016-06-15 pages = extension = .txt mime = text/plain words = 2506 sentences = 133 flesch = 52 summary = 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. The spread of severe acute respiratory syndrome coronavirus (SARS-CoV) from China to Hong Kong and further to Canada was not due to a mass gathering, but to infected individuals travelling late in the incubation period or just after the onset of symptoms. A review in this issue discusses the need for vaccines for mass gatherings and draws attention to immunization against pneumococcal infections in elderly pilgrims and highlights that polio may be a risk. Communicable diseases as health risks at mass gatherings other than Hajj: what is the evidence? cache = ./cache/cord-257200-q0vqlerz.txt txt = ./txt/cord-257200-q0vqlerz.txt === reduce.pl bib === id = cord-268883-nf4fm7r7 author = Corchuelo, Jairo title = Oral manifestations in a patient with a history of asymptomatic COVID-19. Case Report date = 2020-09-01 pages = extension = .txt mime = text/plain words = 1679 sentences = 92 flesch = 49 summary = This case shows that the problems that arise in the oral mucosa in patients with suspected or confirmed SARS-CoV-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technology currently available worldwide. Due to the use of intensified therapeutic methods possibly aggravated by SARS-CoV-2, an increase in cases with oropharyngeal symptoms / conditions, dental-oral problems associated with soft tissues, saliva production (dry mouth) as side effects, could be predicted, even after recovering from COVID-19. Taking into account that Candida albicans is part of the oral microbiome and that there were favorable events for its pathological development, such as the decrease in salivation manifested in the patient by the sensation of dry mouth, in addition to the frequent use of antibiotics and a mild predisposing factor such as the female sex (Zegarelli 1993) and the successful response to nystatin treatment, we can clinically confirm candida infection The hyperpigmentation of the gums in the anterior teeth due to the aesthetic problem that it represents for the patient is the one that causes of most concern. cache = ./cache/cord-268883-nf4fm7r7.txt txt = ./txt/cord-268883-nf4fm7r7.txt === reduce.pl bib === id = cord-253102-z15j8izi author = Ross, Allen G.P. title = Planning for the Next Global Pandemic date = 2015-08-04 pages = extension = .txt mime = text/plain words = 2907 sentences = 171 flesch = 54 summary = The West African Ebola virus pandemic has shown us yet again that the world is ill prepared to respond to a global health emergency. The national health systems in West Africa, and for most low and middle income countries (LMICs), would not meet IHR standards (despite claims by some member WHA nations) and it is unlikely that following the Ebola pandemic much will change. This editorial discusses many issues including priority emerging and reemerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the One Health approach to future pandemic planning. The PEF would 22 If the WHO contingency fund (100 million US dollars) and the World Bank pandemic emergency facility cannot be utilised to strengthen national health systems in LMICs in order to meet IHRs core capabilities, then how can this be achieved? cache = ./cache/cord-253102-z15j8izi.txt txt = ./txt/cord-253102-z15j8izi.txt === reduce.pl bib === id = cord-291638-oatrjbo3 author = Kang, Dayun title = Spatial epidemic dynamics of the COVID-19 outbreak in China date = 2020-04-03 pages = extension = .txt mime = text/plain words = 2637 sentences = 160 flesch = 59 summary = This study described the spatio-temporal pattern and measured the spatial association of the early stages of the COVID-19 epidemic in mainland China from 16 January–06 February 2020. The results showed that most of the models, except medical-care-based connection models, indicated a significant spatial association of COVID-19 infections from around 22 January 2020. There are 31 provinces in mainland China, and this study used 3 weeks' data from 16 January to 06 February 2020, which was during the early stages of COVID-19 in China. Because COVID-19 spread from Hubei Province, the epicentre of the outbreak, the number of newly confirmed cases in the provinces neighbouring Hubei was investigated. It used Moran's I statistic, a measure of spatial association, for the number of confirmed cases with different types of neighbourhoods. On 22 January Models 1-4 first detected a significant spatial dependency on the number of newly confirmed cases. Since approximately 24 January, the number of newly confirmed cases show significant spatial dependency in Models 1 and 2. cache = ./cache/cord-291638-oatrjbo3.txt txt = ./txt/cord-291638-oatrjbo3.txt === reduce.pl bib === id = cord-266253-oyid5haj author = Al-Abaidani, I.S. title = Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman date = 2014-10-29 pages = extension = .txt mime = text/plain words = 1108 sentences = 57 flesch = 53 summary = Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. cache = ./cache/cord-266253-oyid5haj.txt txt = ./txt/cord-266253-oyid5haj.txt === reduce.pl bib === id = cord-258250-zueo1xfa author = Hirotsu, Yosuke title = Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3105 sentences = 184 flesch = 55 summary = title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . cache = ./cache/cord-258250-zueo1xfa.txt txt = ./txt/cord-258250-zueo1xfa.txt === reduce.pl bib === id = cord-008219-ng9xb46c author = Lassmann, Britta title = Highlights from the 6(th) International Meeting on Emerging Diseases and Surveillance (IMED 2016) Vienna, Austria from Nov 3 to 7, 2016 date = 2016-12-09 pages = extension = .txt mime = text/plain words = 2518 sentences = 131 flesch = 47 summary = c o m / l o c a t e / i j i d During the oral abstract presentation session on One Health -Diseases Across Species Boundaries, Toph Allen from EcoHealth Alliance and colleagues shared results from an updated model assessing the global distribution of zoonotic emerging infectious disease risk. Professor [ 1 7 _ T D $ D I F F ] Daniel Lucey summarized the commissions' recommendations including the importance of strengthening national health systems, consolidating and strengthening World Health Organization (WHO) emergency and outbreak response activities, and enhancing research and development. In a separate session, the challenges posed by climate change on infectious disease outbreaks and how to best prevent and track diseases in mobile populations were discussed. The importance of the food chain as a source for emergence and spread of antimicrobial resistance between animals and humans was highlighted in a nation-wide study in Lebanon. cache = ./cache/cord-008219-ng9xb46c.txt txt = ./txt/cord-008219-ng9xb46c.txt === reduce.pl bib === id = cord-254377-j8e8gb0l author = Ali, Sadaf title = Acute cor pulmonale from saddle pulmonary embolism in a patient with previous Covid-19 – should we prolong prophylactic anticoagulation? date = 2020-06-13 pages = extension = .txt mime = text/plain words = 1447 sentences = 87 flesch = 43 summary = However, the risk associated with mild and moderate illness from Covid-19 is unknown, and there is no current recommendation for prophylaxis against thromboembolism in patients after hospital treatment unless there are established thrombophilic risk factors. We report the case of a 52-year old woman, who presented with massive saddle pulmonary embolism after one week of initial hospital discharge, successfully thrombolysed that raises the question of consideration of extended prophylactic anticoagulation even in low risk Covid-19 cases. 3 We report a case of acute massive PE successfully managed by thrombolysis in a patient who was discharged after one week of initial hospital treatment for Covid-19 pneumonia which raises serious concerns about the indication for extended prophylactic anticoagulation in such cases. Emerging data and clinical experience suggest an increased prevalence of venous thromboembolic events (VTE) in COVID-19, especially in patients with severe disease requiring hospitalization, and even among those who are not critically ill. cache = ./cache/cord-254377-j8e8gb0l.txt txt = ./txt/cord-254377-j8e8gb0l.txt === reduce.pl bib === id = cord-024631-yvek5vjz author = Althaus, T. title = Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4327 sentences = 226 flesch = 43 summary = OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. In this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in Southeast Asia, and to evaluate the performance of CRP for discriminating between bacteria and viruses. Specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of C-reactive protein (CRP) testing on antibiotic prescription in primary care [38] . We investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of CRP in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. Investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. cache = ./cache/cord-024631-yvek5vjz.txt txt = ./txt/cord-024631-yvek5vjz.txt === reduce.pl bib === id = cord-254776-m4makxr8 author = Luo, Shiua title = A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China date = 2020-06-01 pages = extension = .txt mime = text/plain words = 384 sentences = 32 flesch = 62 summary = title: A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China The 2019 novel coronavirus disease (COVID-19) epidemic has clearly entered a new stage with rapid spread in countries outside China [1] . Currently, a large number of COVID-19 patients in Wuhan have been cured and discharged. In Wuhan, China, all cured patients with COVID-19 are required to quarantine in either a designated hotel room or at home for 14 days [3] . We retrospectively evaluated the data of the recovered patients with COVID-19 in two different designated fever clinics in Wuhan, with a goal to provide relevant information about these patients. In this study, only 7.7‰ patients experienced recurrence during isolation and observation, and all presented with mild symptoms. Serological tests to identify antibodies played a key role in surveillance of recurrence of COVID-19 [4] . Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) cache = ./cache/cord-254776-m4makxr8.txt txt = ./txt/cord-254776-m4makxr8.txt === reduce.pl bib === id = cord-297396-r1p7xn3a author = Ng, Ming-Yen title = Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3251 sentences = 182 flesch = 53 summary = OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.  Developed two simple-to use nomograms for identifying COVID-19 positive patients  Probabilities are provided to allow healthcare leaders to decide suitable cut-offs  Variables are age, white cell count, chest x-ray appearances and contact history  Model variables are easily available in the general hospital setting. To develop: (1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. Thus, a COVID-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such RT-PCR availability is constrained. cache = ./cache/cord-297396-r1p7xn3a.txt txt = ./txt/cord-297396-r1p7xn3a.txt === reduce.pl bib === id = cord-279976-juz9jnfk author = Xie, Mingxuan title = Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date = 2020-04-01 pages = extension = .txt mime = text/plain words = 3863 sentences = 228 flesch = 50 summary = METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". cache = ./cache/cord-279976-juz9jnfk.txt txt = ./txt/cord-279976-juz9jnfk.txt === reduce.pl bib === id = cord-290100-wnjjqqn5 author = Wong, Samuel Y.S. title = Primary care physicians’ response to pandemic influenza in Hong Kong: a mixed quantitative and qualitative study date = 2012-07-11 pages = extension = .txt mime = text/plain words = 3951 sentences = 186 flesch = 52 summary = OBJECTIVES: The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. RESULTS: We found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among GOPC doctors during the study period. The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. cache = ./cache/cord-290100-wnjjqqn5.txt txt = ./txt/cord-290100-wnjjqqn5.txt === reduce.pl bib === id = cord-280627-dfnc9g2c author = Wang, Xiong title = Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date = 2020-04-18 pages = extension = .txt mime = text/plain words = 1846 sentences = 111 flesch = 53 summary = The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). cache = ./cache/cord-280627-dfnc9g2c.txt txt = ./txt/cord-280627-dfnc9g2c.txt === reduce.pl bib === id = cord-280060-gzby85u9 author = Rello, Jordi title = Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() date = 2016-04-28 pages = extension = .txt mime = text/plain words = 5493 sentences = 297 flesch = 38 summary = 2 A International Journal of Infectious Diseases 48 (2016) 104-112 significant number of immunocompromised patients may also be migrants who may return to their countries of origin to visit friends and relatives, and may acquire travel-associated infections. 26 Cases of Chagas disease (Trypanosoma cruzi) either as a consequence of reactivation of a latent infection not identified at the time of transplant (because an unrecorded travel history or stay in an endemic area) or by transmission through the organ donor, can also be associated with a high mortality. There have also been case reports of severe disease from other travel-associated infections, such as salmonellosis, Vibrio parahaemolyticus, and visceral leishmaniasis in immunocompromised patients. Less common pathogens such as Staphylococcus aureus, avian influenza viruses such as H7N9 and H5N1, the Middle East respiratory syndrome coronavirus (MERS-CoV), and Gram-negative rods such as Burkholderia pseudomallei must also be considered, as well as a few other pathogens that do not usually cause pneumonia, such as malaria. cache = ./cache/cord-280060-gzby85u9.txt txt = ./txt/cord-280060-gzby85u9.txt === reduce.pl bib === id = cord-297715-qcwp2jdv author = Machida, Masaki title = Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak date = 2020-05-17 pages = extension = .txt mime = text/plain words = 2152 sentences = 111 flesch = 48 summary = title: Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak Participants were asked how often they implemented the 5 personal protective measures recommended by the World Health Organization (hand hygiene, social distancing, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) in the baseline and follow-up surveys. In that study, we found that in the early phase of COVID-19 there was J o u r n a l P r e -p r o o f low prevalence among ordinary Japanese citizens in the implementation of social distancing measures and avoiding touching the eyes, nose and mouth, 2 of the 5 personal protective measures recommended by the World Health Organization (WHO) (WHO, 2020a The company, then invited the 2,400 respondents of the baseline survey to participate in a follow-up survey by email on April 1, 2020. cache = ./cache/cord-297715-qcwp2jdv.txt txt = ./txt/cord-297715-qcwp2jdv.txt === reduce.pl bib === id = cord-275250-ilmgy7ce author = Xia, Yong title = Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date = 2020-05-17 pages = extension = .txt mime = text/plain words = 728 sentences = 52 flesch = 63 summary = As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. cache = ./cache/cord-275250-ilmgy7ce.txt txt = ./txt/cord-275250-ilmgy7ce.txt === reduce.pl bib === id = cord-261058-yu2qw02l author = Burgner, David title = Kawasaki disease: What is the epidemiology telling us about the etiology? date = 2005-06-03 pages = extension = .txt mime = text/plain words = 5144 sentences = 324 flesch = 40 summary = Thus in genetically susceptible children, acute infections such as those causing fever and rash, may result in unrecognised damage to the cardiovascular system that later manifests itself as adult cardiovascular disease. 3 The consensus view is that KD results from a widely distributed infectious agent (or possibly agents) that causes the clinical syndrome in genetically susceptible children. Kawasaki disease is more common in boys (male:female ratio 1.6:1) 1 a feature observed in many infectious diseases 30, 31 and also in coronary atherosclerosis, where sex differences in immune responses are suggested to mediate susceptibility. A recent report of an association between the presence of genetic material from a novel coronavirus and Kawasaki disease in a handful of cases 48 remains unproven and may reflect an epiphenomenon; the putative etiological agent is a relatively common viral pathogen in young children and it is unclear how long the DNA persists. cache = ./cache/cord-261058-yu2qw02l.txt txt = ./txt/cord-261058-yu2qw02l.txt === reduce.pl bib === id = cord-283812-ocfjj79v author = Blumberg, Lucille title = Hosting of mass gathering sporting events during the 2013–2016 Ebola virus outbreak in West Africa: experience from three African countries date = 2016-06-15 pages = extension = .txt mime = text/plain words = 2834 sentences = 125 flesch = 46 summary = • The 2013–2016 Ebola virus disease (EVD) outbreak in West Africa that resulted in over 28 637 cases and 11 315 deaths required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of EVD. 7, 8 The unprecedented Ebola virus disease (EVD) epidemic in West Africa 9 and the ongoing Zika virus (ZIKV) outbreak in South America 10, 11 were declared Public Health Emergencies of International Concern (PHEIC) by the World Health Organization (WHO) in August 2014 and February 2016, respectively. 4, 14, 15 The 2013-2016 EVD outbreak in West Africa, which resulted in over 28 637 cases and 11 315 deaths, 16 required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of viral haemorrhagic fever (VHF). cache = ./cache/cord-283812-ocfjj79v.txt txt = ./txt/cord-283812-ocfjj79v.txt === reduce.pl bib === id = cord-301079-n1nytr6k author = Tan, Li title = Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date = 2020-07-27 pages = extension = .txt mime = text/plain words = 3556 sentences = 205 flesch = 60 summary = Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. cache = ./cache/cord-301079-n1nytr6k.txt txt = ./txt/cord-301079-n1nytr6k.txt === reduce.pl bib === id = cord-300583-0krbrj4w author = Koh, Wee Chian title = Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3743 sentences = 207 flesch = 52 summary = METHODS: We identified three distinct physical distancing measures with varying intensity and implemented at different times—international travel controls, restrictions on mass gatherings, and lockdown-type measures—based on the Oxford COVID-19 Government Response Tracker. INTERPRETATION: A combination of physical distancing measures, if implemented early, can be effective in containing COVID-19—tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak. is the average reproduction number of country over the 14 days following the date of the 100 th case; is country 's physical distancing measure of type on the date of the 100 th case; represents the country characteristic (income level, population density, age structure, and temperature) of country ; is a constant term, 's are the regression coefficients, and denotes the error term. cache = ./cache/cord-300583-0krbrj4w.txt txt = ./txt/cord-300583-0krbrj4w.txt === reduce.pl bib === id = cord-305788-z75yv88e author = Agergaard, Charlotte Nielsen title = Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date = 2020-09-28 pages = extension = .txt mime = text/plain words = 727 sentences = 64 flesch = 61 summary = Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. cache = ./cache/cord-305788-z75yv88e.txt txt = ./txt/cord-305788-z75yv88e.txt === reduce.pl bib === id = cord-288167-976qxja2 author = Park, Wan Beom title = Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date = 2018-05-09 pages = extension = .txt mime = text/plain words = 1373 sentences = 87 flesch = 52 summary = title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. In the present study, replicative MERS-CoV was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in MERS-CoV-infected patients with severe pneumonia. In conclusion, replicative MERS-CoV was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic RNA. In upper respiratory tract specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. Middle East respiratory syndrome coronavirus (MERS-CoV) genomic RNA (upE) titers in sputum and transtracheal aspirates with vs. cache = ./cache/cord-288167-976qxja2.txt txt = ./txt/cord-288167-976qxja2.txt === reduce.pl bib === id = cord-292988-q1yz9y8k author = Zumla, Alimuddin title = Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3157 sentences = 174 flesch = 39 summary = title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . cache = ./cache/cord-292988-q1yz9y8k.txt txt = ./txt/cord-292988-q1yz9y8k.txt === reduce.pl bib === id = cord-278406-n5e3a09i author = Macauley, Precious title = CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1492 sentences = 79 flesch = 39 summary = Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). cache = ./cache/cord-278406-n5e3a09i.txt txt = ./txt/cord-278406-n5e3a09i.txt === reduce.pl bib === id = cord-306682-01q775up author = Vijgen, Leen title = Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date = 2004-06-22 pages = extension = .txt mime = text/plain words = 2965 sentences = 166 flesch = 54 summary = In this study we examined whether polymorphisms could be detected in the HCoV-229E binding domain of APN in a Caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in HCoV-229E attachment to human cells. A total of 100 healthy unrelated Belgian individuals were screened for polymorphisms in the human aminopeptidase N domain that is essential for its HCoV-229E receptor activity. All individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the APN gene. In our search for polymorphisms in the APN domain that is essential for its HCoV-229E receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. Three polymorphisms in APN exon 4 (C956T, G978T and G987A) in association with an intron 3 variation (C389T), were identified at a relatively high allele frequency (8.5%) in our Belgian population. cache = ./cache/cord-306682-01q775up.txt txt = ./txt/cord-306682-01q775up.txt === reduce.pl bib === id = cord-260518-mswb3q67 author = Zumla, Alimuddin title = Taking forward a ‘One Health’ approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential date = 2016-06-15 pages = extension = .txt mime = text/plain words = 4039 sentences = 188 flesch = 43 summary = Since the Kingdom of Saudi Arabia is host to millions of pilgrims each year travelling from all continents, 29 tackling the threat of MERS and other infectious diseases with epidemic potential will require enhanced closer cooperation between those who provide human health, animal health, and environmental health services, locally, nationally, regionally, and internationally: the Middle Eastern, European, African, Asian, and American governments, veterinary groups, the WHO, the Food and Agriculture Organization (FAO), the African Union, the United Nations International Children's Emergency Fund (UNICEF), The World Bank, Office International des Epizooties (OIE), CDC, Public Health England, the newly formed Africa CDC, and funding agencies among others. The persistence of MERS-CoV 4 years since its first discovery has created major opportunities for each of the Middle Eastern and African countries to take leadership of the 'One Health' approach with a view to bringing this under regional and global umbrellas, to tackle new emerging and re-emerging infectious diseases with epidemic potential. cache = ./cache/cord-260518-mswb3q67.txt txt = ./txt/cord-260518-mswb3q67.txt === reduce.pl bib === id = cord-265146-j0n3a4m6 author = Hsieh, Ying-Hen title = Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan date = 2013-02-12 pages = extension = .txt mime = text/plain words = 4147 sentences = 192 flesch = 58 summary = Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. RESULTS: Model fit revealed a two-wave epidemic during April 2004–March 2007. Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. Results: Model fit revealed a two-wave epidemic during April 2004-March 2007. Correlation analysis was performed in an attempt to determine the relationship between the male and female IDUs. The data used here were extracted from the monthly reported HIV case data between April 2004 and March 2007, for a total of 36 months, made available by the Taiwan Centers for Disease Control and Prevention (TCDC) on the TCDC website. The monthly time series data of reported HIV cases for male IDUs, female IDUs, and all IDUs in Taiwan were fit to the Richards model as in Figure 1 and Table 1 The effective reproduction number R was computed for each wave. cache = ./cache/cord-265146-j0n3a4m6.txt txt = ./txt/cord-265146-j0n3a4m6.txt === reduce.pl bib === id = cord-308080-1heu9vuv author = Simulundu, Edgar title = First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date = 2020-10-06 pages = extension = .txt mime = text/plain words = 1714 sentences = 99 flesch = 52 summary = title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient's SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. cache = ./cache/cord-308080-1heu9vuv.txt txt = ./txt/cord-308080-1heu9vuv.txt === reduce.pl bib === id = cord-290206-fmy4zrim author = Lim, Jue Tao title = The Costs of an Expanded Screening Criteria for COVID-19: A Modelling Study date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4208 sentences = 203 flesch = 47 summary = The screening process should therefore maximise sensitivity to minimise the number of missed cases and risk of nosocomial transmission, which occurred in Singapore during another coronavirus outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003. Using ESC, NUH clinicians were able to identify and isolate 13 patients who did not fit the WHO SARS criteria but were eventually confirmed to have SARS, who would have otherwise been potential spreaders (the number of positive and negative cases for SARS are presented in Supplementary Table 1.) 12 Clinicians responded to the COVID-19 crisis similarly, implementing ESC on 7 th February 2020, which was approximately three weeks after the first imported case. At an of 2.5 and incubation period (IP) of 4 days, approximate to estimates by Wu and colleagues 29 for Wuhan, an estimated 240 (95% CI: 200-290) cases would be prevented over 150 days through ESC by isolating patients presenting fever or respiratory symptoms such as cough with their travel and exposure profile not considered (Table 2) . cache = ./cache/cord-290206-fmy4zrim.txt txt = ./txt/cord-290206-fmy4zrim.txt === reduce.pl bib === id = cord-255021-acgfwjwi author = Luo, Ying title = Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus date = 2020-05-01 pages = extension = .txt mime = text/plain words = 595 sentences = 49 flesch = 62 summary = title: Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus Abstract Background The differential diagnosis between novel coronavirus pneumonia patients (NCPP) and influenza patients (IP) remains a challenge in clinical practice. We observed that NCPP had significantly decreased white blood cells, alkaline phosphatase, and d-dimer, compared with IP. Conclusions Some routine laboratory results had statistical difference between NCPP and IP. A diagnostic model based on combination of routine laboratory results provides an adjunct approach in the differential diagnosis between NCPP and IP. We observed that NCPP had 37 significantly decreased white blood cells, alkaline phosphatase, and d-dimer, The Lancet, 2020). Epidemiological and clinical 307 characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a 308 descriptive study Clinical features of patients 312 infected with 2019 novel coronavirus in Wuhan cache = ./cache/cord-255021-acgfwjwi.txt txt = ./txt/cord-255021-acgfwjwi.txt === reduce.pl bib === id = cord-279581-d2l4nnex author = Abuhabib, A.A. title = Unique situation of Gaza Strip dealing with COVID-19 crisis date = 2020-09-03 pages = extension = .txt mime = text/plain words = 1153 sentences = 47 flesch = 45 summary = Constructively, this study follows direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario within a limited time frame covering the period from 22 March to 05 July 2020. This study follows the direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario likelihood determination and consequences identification within a limited time frame covering the period from 22 March to 05 July 2020. cache = ./cache/cord-279581-d2l4nnex.txt txt = ./txt/cord-279581-d2l4nnex.txt === reduce.pl bib === id = cord-303417-1237ykxt author = d’Arminio Monforte, Antonella title = Effectiveness of Hydroxychloroquine in COVID-19 disease: A done and dusted situation? date = 2020-07-29 pages = extension = .txt mime = text/plain words = 659 sentences = 42 flesch = 52 summary = Arshad et al show evidence for a reduced mortality in Covid-19 patients taking hydroxychloroquine alone or with azithromycin in an observational study in USA [1] . We divided a subset of our cohort in three groups who started treatment a median of 1 day after admission: those receiving hydroxycholoroquine alone (N=197), those receiving hydroxycholoroquine+azithromycin (N=94), and those receiving neither (controls) (N=92). After adjusting for a number of key confounders (see table) , the use of hydroxycholoroquine+azithromycin was associated with a 66% reduction in risk of death as compared to controls; the analysis also suggested a larger effectiveness of hydroxychloroquine in patients with less severe COVID-19 disease (PO2/FiO2>300, interaction p-value<.0001). Treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalised with COVID-19 Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomised clinical trial Hydroxychloroquine in patients mainly with mild to moderate COVID-19: an open-label, randomised, controlled trial An observational cohort study of hydroxychloroquine and azithromycin for COVID-19: (Can't get no) satisfaction cache = ./cache/cord-303417-1237ykxt.txt txt = ./txt/cord-303417-1237ykxt.txt === reduce.pl bib === id = cord-260332-tnz6k2z1 author = Tran, Tu Anh title = CT scan does not make a diagnosis of Covid-19: a cautionary case report() date = 2020-09-02 pages = extension = .txt mime = text/plain words = 338 sentences = 28 flesch = 65 summary = key: cord-260332-tnz6k2z1 title: CT scan does not make a diagnosis of Covid-19: a cautionary case report() Here, we report the clinical case of a 12-year-old girl presenting with flu-like symptoms, cough, anosmia, ageusia, breathing difficulties, patchy ground glass opacities on TDM chest scan who turned out to be Coronavirus 229E-infected. This case must draw attention on the risk of false COVID-19 diagnosis when relying overly on CT scan imaging. RT-PCR assays of nasopharyngeal samples at admittance and 24 hours later, were negative for SARS-CoV-2. In this case report, parents' anosmia and ageusia as well as chest scanner could have been misleading. According to Kim et al., scanner screening of patients with suspected COVID-19 in low-prevalence countries has a poor positive prediction value (1%-31%) 2 . The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. cache = ./cache/cord-260332-tnz6k2z1.txt txt = ./txt/cord-260332-tnz6k2z1.txt === reduce.pl bib === id = cord-305782-gnzwe2z2 author = Satici, Celal title = Performance of Pneumonia Severity Index and CURB-65 in Predicting 30-day mortality in patients with COVID-19 date = 2020-06-14 pages = extension = .txt mime = text/plain words = 3363 sentences = 188 flesch = 55 summary = Abstract Objective The aim of the study was to analyze the usefulness of the CURB-65 and pneumonia severity index (PSI) in predicting 30-day mortality in patients with COVID-19 and to identify other factors associated with higher mortality. Conclusion In a large group of hospitalized patients with COVID-19, we found that PSI performed better than CURB-65 in predicting mortality. According to the Health Ministry Guideline, any suspected case who is over 50 years old or has any comorbidity should be hospitalized irrespective of vital signs, laboratory results and computed tomography (CT) findings (Bilim Kurulu, 2020) Thus, a large proportion of patients with COVID-19 meet criteria for admission as an inpatient. In this study, we aimed to assess whether CURB-65 or PSI is useful tool to predict 30-day mortality and to identify other factors that are associated with higher mortality in patients with COVID-19. cache = ./cache/cord-305782-gnzwe2z2.txt txt = ./txt/cord-305782-gnzwe2z2.txt === reduce.pl bib === id = cord-304743-0bsdahh6 author = Kortepeter, Mark G title = Marburg Virus Disease: a Summary for Clinicians date = 2020-08-03 pages = extension = .txt mime = text/plain words = 1327 sentences = 92 flesch = 43 summary = Abstract Objectives This article is a summary of countermeasures for Marburg virus disease focusing on pathogenesis, clinical features, and diagnostics, with an emphasis on therapies and vaccines that have demonstrated potential for use in an emergency situation, through their evaluation in nonhuman primates (NHPs) and/or in humans. Results We identified six treatments and four vaccine platforms that have demonstrated potential benefit for treating or preventing infection in humans, through their efficacy in NHPs. Conclusion We provide succinct summaries of Marburg countermeasures to give the busy clinician a head start in reviewing the literature if faced with a patient with Marburg virus disease. Postexposure protection against Marburg haemorrhagic fever with recombinant vesicular stomatitis virus vectors in non-human primates: an efficacy assessment Vesicular stomatitis virus-based vaccines protect nonhuman primates against aerosol challenge with Ebola and Marburg viruses. Single-injection vaccine protects nonhuman primates against infection with Marburg virus and three species of ebola virus cache = ./cache/cord-304743-0bsdahh6.txt txt = ./txt/cord-304743-0bsdahh6.txt === reduce.pl bib === id = cord-311026-mpr3xb2a author = Petersen, Eskild title = COVID-19–We urgently need to start developing an exit strategy date = 2020-04-29 pages = extension = .txt mime = text/plain words = 5624 sentences = 339 flesch = 56 summary = Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state's strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. cache = ./cache/cord-311026-mpr3xb2a.txt txt = ./txt/cord-311026-mpr3xb2a.txt === reduce.pl bib === id = cord-311413-uiwjrvru author = Chanda-Kapata, Pascalina title = COVID-19 and malaria: A symptom screening challenge for malaria endemic countries date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1734 sentences = 94 flesch = 52 summary = COVID-19 currently imposes an additional burden to the already overstretched, resource strapped health services which are grappling to bring under control the high burden of existing infectious and non-infectious diseases, including TB, HIV, and malaria. Health care workers and community members alike are faced with an important challenge of quickly identifying symptoms and taking appropriate steps for laboratory investigation in line with the case definition based on surveillance or clinical characterisation (WHO, 2020a) . Key steps to identifying a COVID-19 case ultimately involves symptomatic or high risk patients presenting to health providers with complaints of any of the following symptoms or travel history: fever, cough, shortness of breath, fatigue, headache and others of acute onset or history of travel to affected areas or contact with an infected person. Thus, current screening approaches for COVID-19 are likely to miss approximately 50% of the infected cases even in countries with good health systems and available diagnostic capacities (Gostic et al., 2020) . cache = ./cache/cord-311413-uiwjrvru.txt txt = ./txt/cord-311413-uiwjrvru.txt === reduce.pl bib === id = cord-257737-obadq502 author = Wu, Di title = Positive effects of COVID-19 control measures on influenza prevention date = 2020-04-10 pages = extension = .txt mime = text/plain words = 354 sentences = 31 flesch = 75 summary = title: Positive effects of COVID-19 control measures on influenza prevention This article aims to alert clinicians of the presence of co-infection with these two viruses and to describe the effect of the measures taken to fight COVID-19 on influenza prevention and control. [ 4 ] have reported the case of a patient co-infected with SARS-CoV-2 and influenza A virus. Also, Li and Wang [ 5 ] have reported the need to be alert to the superposed effect of seasonal influenza while fighting pneumonia caused by the novel coronavirus. Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention Coronavirus disease 2019 (COVID-19) Situation Report -71 Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia Be alert to superposed effect of seasonal influenza while fighting against novel coronavirus pneumonia cache = ./cache/cord-257737-obadq502.txt txt = ./txt/cord-257737-obadq502.txt === reduce.pl bib === id = cord-261672-0cresfn8 author = Kim, Sungchan title = Evaluation of COVID-19 epidemic outbreak caused by temporal contact-increase in South Korea date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1635 sentences = 108 flesch = 59 summary = OBJECTIVES: On March 15, 2020, 61.3% of the confirmed cases of COVID-19 infection are associated with the worship service that was organized on February 9 in the Shincheonji Church of Jesus in Daegu, South Korea. METHOD: Using opened data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model. The effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on February 9 in the Shincheonji Church of Jesus, Daegu. However, the effective reproduction number decreased to less than unity after February 28 owing to the implementation of high-level preventive control interventions in South Korea, coupled with voluntary prevention actions by citizens. In this study, we aimed to evaluate the effects of mass infection due to temporal increases in contacts and assess the preventive control interventions using the confirmed cases and deaths data associated with COVID-19 in Korea. cache = ./cache/cord-261672-0cresfn8.txt txt = ./txt/cord-261672-0cresfn8.txt === reduce.pl bib === id = cord-282421-yialyuav author = Alcoba-Florez, Julia title = Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date = 2020-08-01 pages = extension = .txt mime = text/plain words = 1049 sentences = 69 flesch = 55 summary = In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. cache = ./cache/cord-282421-yialyuav.txt txt = ./txt/cord-282421-yialyuav.txt === reduce.pl bib === id = cord-274230-old0xmcc author = Zhao, Qianwen title = Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis date = 2020-05-04 pages = extension = .txt mime = text/plain words = 867 sentences = 72 flesch = 56 summary = title: Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis Mean difference (MD) of lymphocyte count in COVID-19 patients with or without severe disease and odds ratio (OR) of lymphopenia for severe form of COVID-19 was evaluated with this meta-analysis. The pooled analysis showed that lymphocyte count was significantly lower in severe COVID-19 patients (MD -0.31×109/L; 95%CI: -0.42 to -0.19×109/L). After the significant clinical heterogeneity was excluded, the 130 randomized effects model was used for meta-analysis. Severe Outcomes Among Patients with Coronavirus Disease 2019 (COVID-19) -United States Risk Factors Associated With Acute Respiratory Distress Syndrome 284 and Death in Patients With Coronavirus Disease Retrospective study on the epidemiological 300 characteristics of 139 patients with novel coronavirus pneumonia on the effects of Severity Effects of severe acute respiratory syndrome (SARS) coronavirus 311 infection on peripheral blood lymphocytes and their subsets Lymphopenia predicts disease severity of COVID-19: a 322 descriptive and predictive study cache = ./cache/cord-274230-old0xmcc.txt txt = ./txt/cord-274230-old0xmcc.txt === reduce.pl bib === id = cord-271495-5906wju4 author = Beldomenico, Pablo M. title = Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1995 sentences = 107 flesch = 53 summary = Data and modelling supported the existence of 'superspreaders' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. cache = ./cache/cord-271495-5906wju4.txt txt = ./txt/cord-271495-5906wju4.txt === reduce.pl bib === id = cord-311479-8pjoz64q author = He, Daihai title = The relative transmissibility of asymptomatic cases among close contacts date = 2020-04-18 pages = extension = .txt mime = text/plain words = 815 sentences = 58 flesch = 57 summary = A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. 28 29 Keywords: COVID-19; asymptomatic cases; relative transmissibility 30 31 32 33 Main text 35 Nishiura et al (Nishiura et al, 2020 ) estimated the asymptomatic ratio of COVID-19 was 41.6% 36 (5 out of 12 confirmed cases) among 565 Japanese individuals evacuated from Wuhan, China. The odds ratio (OR) is estimated 109 In summary, we conclude that the relatively transmissibility of asymptomatic case could be 127 significantly smaller than that of the symptomatic cases. Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-158 19) Estimating the asymptomatic 161 proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess 162 cruise ship cache = ./cache/cord-311479-8pjoz64q.txt txt = ./txt/cord-311479-8pjoz64q.txt === reduce.pl bib === id = cord-289304-9srk0ohb author = Bagnato, Sergio title = Critical illness myopathy after COVID-19 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1723 sentences = 98 flesch = 48 summary = We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 (COVID-19). We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 . The patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (EMG) of the proximal and distal muscles, and direct muscle stimulation (DMS). In this report, we describe neurophysiological findings from a patient who developed severe muscular weakness, likely due to CIM, after hospitalization for COVID-19. The patient described here had myopathy, with greater involvement of the proximal muscles in the lower limbs, probably reflecting ICU-acquired weakness. Since rehabilitation programs can be effective to reverse muscle weakness caused by CIM, health systems must plan to provide adequate access to rehabilitative facilities for patients requiring both pulmonary and motor rehabilitative treatment after COVID-19. cache = ./cache/cord-289304-9srk0ohb.txt txt = ./txt/cord-289304-9srk0ohb.txt === reduce.pl bib === id = cord-292092-o6s5nw49 author = Furuse, Yuki title = Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date = 2015-09-30 pages = extension = .txt mime = text/plain words = 1232 sentences = 77 flesch = 60 summary = title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. 5 The laboratory diagnosis of MERS-CoV infection is mainly performed using real-time reverse transcription PCR (RT-PCR) to detect viral RNA in specimens. This study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the RT-PCR protocols for the molecular diagnosis of MERS-CoV infections. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Table 1 Conservation of the primer and probe region sequences of the WHO-recommended assays for the molecular diagnosis of MERS-CoV cache = ./cache/cord-292092-o6s5nw49.txt txt = ./txt/cord-292092-o6s5nw49.txt === reduce.pl bib === id = cord-275191-lgze4zex author = Al-Sadeq, Duaa W. title = The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3287 sentences = 221 flesch = 48 summary = AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. cache = ./cache/cord-275191-lgze4zex.txt txt = ./txt/cord-275191-lgze4zex.txt === reduce.pl bib === id = cord-274028-dvsvtsn0 author = Del Brutto, Oscar H. title = SARS-CoV-2-related mortality in a rural Latin American population date = 2020-08-08 pages = extension = .txt mime = text/plain words = 1217 sentences = 74 flesch = 60 summary = Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . cache = ./cache/cord-274028-dvsvtsn0.txt txt = ./txt/cord-274028-dvsvtsn0.txt === reduce.pl bib === id = cord-304872-hnxmtbrf author = Lv, Hao title = Prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with COVID‑19 in Wuhan, China date = 2020-09-17 pages = extension = .txt mime = text/plain words = 3433 sentences = 204 flesch = 56 summary = OBJECTIVES: To investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (COVID-19) in Wuhan using a telephone interview. The characteristics of the patient's disease course and recovery time for olfactory and/or gustatory dysfunctions (OD and/or GD) were collected by telephone interview. Two hypotheses might explain the low prevalence of OD and/ or GD reported in the Chinese study: First, the number of Chinese patients with COVID-19 who exhibit olfactory or gustatory disorders is indeed lower. Furthermore, all previous studies were limited to the acute phase with a short follow-up period, which might not reflect the recovery regularity of olfactory and/or gustatory impairment in patients with COVID 19. The aim of this study was to investigate the occurrence and recovery time of olfactory and/or gustatory dysfunction in patients with COVID-19 infection who were discharged from non-intensive care units 3 months earlier in China. cache = ./cache/cord-304872-hnxmtbrf.txt txt = ./txt/cord-304872-hnxmtbrf.txt === reduce.pl bib === id = cord-259837-5tbdqzxr author = Kalcioglu, Mahmut Tayyar title = May COVID-19 cause sudden sensorineural hearing loss? date = 2020-09-29 pages = extension = .txt mime = text/plain words = 519 sentences = 38 flesch = 59 summary = title: May COVID-19 cause sudden sensorineural hearing loss? In previous studies, viral infections have been reported to have an important role in the etiology of sudden sensorineural hearing loss (SSNHL) (Cohen et al., 2014) . Moreover, recently, studies on the effects of SARS-CoV-2 virus on central and peripheral nervous systems have been published. Some of these studies have reported Guillain -Barré syndrome (Toscano et al., 2020) and impaired olfactory function (Eliezer et al., 2020) to be related to SARS-CoV-2. Another recently published study reported neurologic changes in 58 of 64 patients with COVID-19 (Helms et al., 2020) . Therefore, we investigated the possibility of SARS-CoV-2 infection in these J o u r n a l P r e -p r o o f patients. Sudden and Complete Olfactory Loss Function as a Possible Symptom of COVID-19 An investigation into SARS-COV-2 in the etiology of sudden sensorineural hearing loss cache = ./cache/cord-259837-5tbdqzxr.txt txt = ./txt/cord-259837-5tbdqzxr.txt === reduce.pl bib === id = cord-311453-l6quzef6 author = Klopfenstein, Timothée title = Impact of Tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 COVID-19 patients date = 2020-08-13 pages = extension = .txt mime = text/plain words = 2675 sentences = 154 flesch = 55 summary = CONCLUSION: Despite the small sample size in the group TCZ, this result suggests that TCZ reduces mortality and/or IMV requirement in patients with severe SARS-CoV-2 pneumonia. We have recently published a retrospective study including 45 patients treated in our hospital, which shows that TCZ seems to reduce the number of COVID-19 severe cases and/or mortality (11) . Based on the medical literature, we checked several criteria before starting TCZ treatment: no contraindication to TCZ, confirmed COVID-19 with real-time reverse transcription (RT)-PCR SARS-CoV-2 RNA, failure of standard treatment, period since symptoms onset ≥ 5 days, oxygen therapy ≥ 4 liters/min, ≥ 25% of lung damages on chest computed tomography (CT) scan, and ≥ 2 parameters of inflammation or biological markers of mortality (with a high level) such as ferritin, CRP, D-dimer, lymphopenia, and/or lactate dehydrogenase. cache = ./cache/cord-311453-l6quzef6.txt txt = ./txt/cord-311453-l6quzef6.txt === reduce.pl bib === id = cord-276445-m5vjo3ym author = Lee, Hyojung title = Recrudescence of Ebola virus disease outbreak in West Africa, 2014–2016 date = 2017-09-20 pages = extension = .txt mime = text/plain words = 1632 sentences = 88 flesch = 54 summary = For the Ebola virus disease (EVD) outbreak in West Africa from 2014 to 2016, the World Health Organization (WHO) recommended securing 42 days (World Health Organization, 2015) , or twice the observed maximum incubation period, from the time at which the last case was found negative for the virus at second testing. WHO reports and other sources were reviewed in an analysis of all known recrudescence events occurring from 2014 to 2016 (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . A total of five cases of recrudescence were identified ( Figure 1 ): three occurred in Liberia and one each in Guinea and Sierra Leone (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . cache = ./cache/cord-276445-m5vjo3ym.txt txt = ./txt/cord-276445-m5vjo3ym.txt === reduce.pl bib === === reduce.pl bib === id = cord-273090-fdzkfo1u author = He, Susu title = Relationship between Chest CT manifestations and immune response in COVID-19 patients date = 2020-06-20 pages = extension = .txt mime = text/plain words = 2816 sentences = 140 flesch = 58 summary = In critically ill patients, the decrease of absolute value of CD4 + T cells and increase of IL-6 level are significantly correlated with the volume of lung lesions. There have been many reports that most of the 2019-nCoV patients have chest CT manifestations of pneumonia, typically showing bilateral ground-glass shadows and patchy shadows, and a few can also appear as consolidation shadows and interstitial lesions, the laboratory showed that the lymphocytes count in most patients decreased [6] [7] [8] [9] , with gradually worsened the disease, the lymphocytes absolute count continued to decline [9] , and has been There are reports in the literature that the proinflammatory cytokines IL-2, IL-6, IL-8, IL-10, and TNF-α are elevated in some 2019-nCoV patients [7] [8] . The purpose of this study is to investigate changes in lymphocytes counts and cytokines levels induced by 2019-nCoV and their effects on lung lesions, to determine the severity of the disease, and to select markers that could prompt early clinical intervention. cache = ./cache/cord-273090-fdzkfo1u.txt txt = ./txt/cord-273090-fdzkfo1u.txt === reduce.pl bib === id = cord-308114-68cgub5o author = Afrin, Lawrence B. title = Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3455 sentences = 186 flesch = 45 summary = MCs, present in all vascularized tissues but dominantly at the environmental interfaces and in vessel walls (Akin and Metcalfe, 2004) , are activated by the SARS-Cov-2 coronavirus which causes Covid-19 infection (Kritas et al., 2020; Theoharides, 2020; Zhou et al., 2020) , leading to MC activation and resulting release of various subsets of the MC's >1000 potent multi-action mediators (Ibelgaufts, 2020) (including biogenic amines (e.g., histamine), proteases (e.g., tryptase and chymase), cytokines (e.g., interleukins and TNF-α), eicosanoids (e.g., prostaglandins and leukotrienes), heparin, and growth factors) increasingly thought to play a key role in driving the hyperinflammation of severe Covid-19 illness (Kempuraj et al., 2020; Valent et al., 2020) . cache = ./cache/cord-308114-68cgub5o.txt txt = ./txt/cord-308114-68cgub5o.txt === reduce.pl bib === id = cord-293942-n5ypkftc author = Takoi, Hiroyuki title = Favipiravir-induced fever in coronavirus disease 2019: A report of two cases date = 2020-09-28 pages = extension = .txt mime = text/plain words = 1160 sentences = 76 flesch = 54 summary = title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases Favipiravir, an antiviral agent, is undergoing clinical trials for treating novel coronavirus disease 2019 (COVID-19). We report two cases of COVID-19 with favipiravir-induced fever. Favipiravir, a promising antiviral agent, is undergoing clinical trials as an alternative drug for treating COVID-19 (Arab-Zozani et al., 2020) in several countries, including China (Chen et al., 2020) , Iran, Germany, and Japan. We experienced two cases of favipiravir-induced fever in patients hospitalized with COVID-19. Drug-induced fever was suspected and favipiravir was discontinued on Day 10. This preliminary report may help differentiate paradoxical fever in patients receiving favipiravir therapy for COVID-19. Favipiravir for treating patients with novel coronavirus (COVID-19): protocol for a systematic review and meta-analysis of randomised clinical trials Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: A case series cache = ./cache/cord-293942-n5ypkftc.txt txt = ./txt/cord-293942-n5ypkftc.txt === reduce.pl bib === id = cord-277640-vy7ex5lv author = Calderaro, Adriana title = SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1171 sentences = 63 flesch = 52 summary = The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. cache = ./cache/cord-277640-vy7ex5lv.txt txt = ./txt/cord-277640-vy7ex5lv.txt === reduce.pl bib === id = cord-293630-zc8huo1j author = Capone, Alessandro title = Simultaneous circulation of COVID-19 and flu in Italy: potential combined effects on the risk of death? date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2157 sentences = 97 flesch = 43 summary = Based on data updated to May 20, 2020, in Italy the total recorded number of patients who died due to COVID-19-related reasons is 31,851. While some of the excess mortality reported in the ILI group may be attributable to COVID-19, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? It would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from COVID-19 or influenza. While some of the excess mortality reported in the ILI group (in over 65) may be attributable to COVID-19 infection actually, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? cache = ./cache/cord-293630-zc8huo1j.txt txt = ./txt/cord-293630-zc8huo1j.txt === reduce.pl bib === id = cord-310691-6danlh8h author = Ma, Simin title = Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date = 2020-05-26 pages = extension = .txt mime = text/plain words = 2297 sentences = 149 flesch = 57 summary = title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. cache = ./cache/cord-310691-6danlh8h.txt txt = ./txt/cord-310691-6danlh8h.txt === reduce.pl bib === id = cord-257265-lkzytud0 author = Zheng, Fang title = SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date = 2020-08-03 pages = extension = .txt mime = text/plain words = 4181 sentences = 236 flesch = 53 summary = According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. cache = ./cache/cord-257265-lkzytud0.txt txt = ./txt/cord-257265-lkzytud0.txt === reduce.pl bib === id = cord-301085-tk2vvxj7 author = Askarian, Mehrdad title = Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran date = 2006-07-11 pages = extension = .txt mime = text/plain words = 2610 sentences = 137 flesch = 42 summary = title: Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. [2] [3] [4] The purpose of our study was to measure the level of knowledge, attitude, and practice in surgeons and physicians in Shiraz University of Medical Sciences affiliated hospitals. cache = ./cache/cord-301085-tk2vvxj7.txt txt = ./txt/cord-301085-tk2vvxj7.txt === reduce.pl bib === id = cord-279892-37vyazby author = Sun, Guanghao title = Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases date = 2017-01-16 pages = extension = .txt mime = text/plain words = 2904 sentences = 154 flesch = 47 summary = This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. These systems have already been installed at most major international airports, and they can remotely sense several vital signs, including body temperature and heart and respiration rates, thereby facilitating the rapid and accurate screening of people who are suspected of carrying infectious diseases. To distinguish between patients with infectious influenza and healthy control subjects, logistic regression discriminant analysis was used to establish a classification model based on the three derived vital signs. The classification model was established using the data that described the three vital signs from the 16 influenza virus-infected patients and the 22 healthy control subjects using multivariable logistic regression. cache = ./cache/cord-279892-37vyazby.txt txt = ./txt/cord-279892-37vyazby.txt === reduce.pl bib === id = cord-283891-m36un1y2 author = Hu, Bisong title = First, second and potential third generation spreads of the COVID-19 epidemic in mainland China: an early exploratory study incorporating location-based service data of mobile devices date = 2020-05-17 pages = extension = .txt mime = text/plain words = 4656 sentences = 220 flesch = 47 summary = Methods We used spatiotemporal data of COVID-19 cases in mainland China and two categories of location-based service (LBS) data of mobile devices from the primary and secondary epidemic sources to calculate Pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. Here, using location-based service (LBS) data of mobile devices, we analyzed the spatiotemporal association of the confirmed COVID-19 cases and human movements from the sources of the epidemic outbreak, and revealed the first, second and potential third generation spreads of the COVID-19 epidemic in mainland China. Based on the above datasets of COVID-19 cases in mainland China and two categories of location-based service data of mobile devices from the epidemic sources, we calculated their Pearson correlation coefficient, r, and spatial stratified heterogeneity (SSH), q, statistics. cache = ./cache/cord-283891-m36un1y2.txt txt = ./txt/cord-283891-m36un1y2.txt === reduce.pl bib === id = cord-291367-rtmsrh16 author = Zumla, Alimuddin title = Middle East Respiratory Syndrome - need for increased vigilance and watchful surveillance for MERS-CoV in sub-Saharan Africa date = 2015-07-02 pages = extension = .txt mime = text/plain words = 2262 sentences = 119 flesch = 50 summary = 4, 5 The recent unprecedented outbreak of the MERS 6, 7 in South Korea which arose consequential to the importation of MERS-CoV by a South Korean traveler to the Middle East, alarmed global public health authorities and highlights the potential of MERS-CoV to spread across the globe and cause local outbreaks. National surveillance systems should be on alert for the low but long-lasting risk of MERS-CoV infected pilgrims returning from the Umrah throughout the year, and also for the large numbers of refugees at several conflict zones in the Middle East (those migrating from Syria to Turkey and from the Yemen border into Saudi Arabia and beyond). The Hajj pilgrimage and surveillance for Middle East Respiratory syndrome coronavirus in pilgrims from African countries Infection prevention and control during health care for probable or confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. cache = ./cache/cord-291367-rtmsrh16.txt txt = ./txt/cord-291367-rtmsrh16.txt === reduce.pl bib === id = cord-286743-z0e5arlm author = Langer-Gould, Annette title = Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4258 sentences = 213 flesch = 43 summary = Subsequently, a shift in practice by clinicians at some of our medical centers aimed to identify early COVID19-CS through laboratory abnormalities in patients with increasing O2 requirements and to initiate combined treatment with anakinra and corticosteroids occurred. Data were extracted by manual reviewing the EHR, including onset of dyspnea and other COVID-19 symptoms, age, sex, comorbidities, smoking status, tocilizumab and anakinra use, other J o u r n a l P r e -p r o o f treatments rendered for hydroxychloroquine, and/or corticosteroids) , fever (>100.4F), hypotension requiring pressors, dates of admission, intubation, extubation, discharge and/or death. The primary purpose of analyses was to describe clinical outcomes among tocilizumab-or anakinra-treated COVID-19 patients and to examine whether differences in outcomes could be accounted for by COVID19-CS severity and/or duration at the time of treatment initiation (baseline). cache = ./cache/cord-286743-z0e5arlm.txt txt = ./txt/cord-286743-z0e5arlm.txt === reduce.pl bib === id = cord-287209-hkrarxsd author = Zhao, Shi title = The basic reproduction number of novel coronavirus (2019-nCoV) estimation based on exponential growth in the early outbreak in China from 2019 to 2020: A reply to Dhungana date = 2020-02-20 pages = extension = .txt mime = text/plain words = 941 sentences = 65 flesch = 66 summary = title: The basic reproduction number of novel coronavirus (2019-nCoV) estimation based on exponential growth in the early outbreak in China from 2019 to 2020: A reply to Dhungana The estimates on the basic reproduction number, R0, were carried out in early outbreak as of January 22, 2020 when the surveillance data and the knowledge on the key epidemiological features of 2019-nCoV were limited. The estimates of the basic reproduction number, R0, with varying reporting rates, mean and SD of serial interval (SI). Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak cache = ./cache/cord-287209-hkrarxsd.txt txt = ./txt/cord-287209-hkrarxsd.txt === reduce.pl bib === === reduce.pl bib === id = cord-273961-ja8xggnd author = Nakagawara, Kensuke title = Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date = 2020-07-26 pages = extension = .txt mime = text/plain words = 784 sentences = 54 flesch = 58 summary = title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . cache = ./cache/cord-273961-ja8xggnd.txt txt = ./txt/cord-273961-ja8xggnd.txt === reduce.pl bib === id = cord-300774-5mrkmctl author = Hernández-Mora, Miguel Górgolas title = Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date = 2020-10-25 pages = extension = .txt mime = text/plain words = 4340 sentences = 230 flesch = 50 summary = INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . cache = ./cache/cord-300774-5mrkmctl.txt txt = ./txt/cord-300774-5mrkmctl.txt === reduce.pl bib === id = cord-309032-idjdzs97 author = Zhou, Feng title = Epidemiological Characteristics and Factors Associated with Critical Time Intervals of COVID-19 in Eighteen Provinces, China: A Retrospective Study date = 2020-10-09 pages = extension = .txt mime = text/plain words = 4176 sentences = 237 flesch = 54 summary = Several studies conducted in China, Italy and the United States have reported some epidemiological characteristics of COVID-19 in the initial phase (Grasselli et al., 2020 , Liang et al., 2020 , Price-Haywood et al., 2020 , Richardson et al., 2020 , Wu and McGoogan, 2020 , However, there is still a lack of research on the space-time characteristics in the populations of imported and local cases respectively which is of great significance. In this study, we described the spatiotemporal distribution of the COVID-19 in eighteen provinces of China (outside Hubei province) and investigated the epidemiological characteristics in the population of imported cases and local cases, from the beginning of this epidemic until it was under good control. We further assessed the critical influence factors associated with time interval from symptom onset to hospitalization (TOH) and length of hospital stay (LOS), including demographic and temporal and spatial characteristics. cache = ./cache/cord-309032-idjdzs97.txt txt = ./txt/cord-309032-idjdzs97.txt === reduce.pl bib === id = cord-305763-160heazx author = Lai, Chih-Cheng title = Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date = 2020-10-09 pages = extension = .txt mime = text/plain words = 4257 sentences = 264 flesch = 61 summary = One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. cache = ./cache/cord-305763-160heazx.txt txt = ./txt/cord-305763-160heazx.txt === reduce.pl bib === id = cord-293247-ltxt2dfv author = Elachola, Habida title = Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings date = 2015-10-09 pages = extension = .txt mime = text/plain words = 1233 sentences = 57 flesch = 44 summary = title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings Although current GHSA is yet to specifically highlight mass gathering preparedness as a strategic priority even in countries with high participant contribution to mass gatherings, the 12 Global Health Security Agenda action packages and the strategies to minimize the implications of mass gathering on public health are similar. Given that two-thirds of the emerging diseases are zoonotic, human-animal interaction during some mass gatherings such as the Hajj further increases the risk, and Saudi Arabia imports sacrifice animals from 6 countries. Mass gatherings offer opportunities to implement, test, and assess GHSA objectives in its entirety and can contribute significantly to health security of individuals, nations, and the world. Mass gatherings medicine and global health security cache = ./cache/cord-293247-ltxt2dfv.txt txt = ./txt/cord-293247-ltxt2dfv.txt === reduce.pl bib === id = cord-302409-40ktyt5q author = Wang, Jie title = SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2771 sentences = 166 flesch = 51 summary = OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. cache = ./cache/cord-302409-40ktyt5q.txt txt = ./txt/cord-302409-40ktyt5q.txt === reduce.pl bib === id = cord-292256-jp80u828 author = Moriguchi, Takeshi title = A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1742 sentences = 121 flesch = 53 summary = We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient's nasopharyngeal specimen is negative. cache = ./cache/cord-292256-jp80u828.txt txt = ./txt/cord-292256-jp80u828.txt === reduce.pl bib === id = cord-315059-l6guql8q author = Mubarak, Naeem title = Corona and Clergy: The missing link for an effective social distancing in Pakistan. Time for some unpopular decisions date = 2020-04-30 pages = extension = .txt mime = text/plain words = 475 sentences = 44 flesch = 73 summary = title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. To begin with, more than half of the COVID-19 cases in Malaysia received virus 11 in a congregation of 16000 believers from 30 countries. Pakistan's case is of concern due to a fragile healthcare system, poor hygiene practices, 20 limited access to healthcare, and steep rise in the number of local cases in a population bigger 21 than Italy and Iran combined. Evidence supports the substantial impact of social distancing as 22 a viable practice to contain the spread of the virus. In Pakistan, the practice of social distancing 24 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 Muslim world, and cancelled Umrah (pilgrimage). for Pakistan to implement social distancing in the holy month of Ramadan (26 th April) when 46 influx in mosques increases many-fold for daily prayers and Tarawih (an additional prayer in 47 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 79 80 COVID-19: Pakistan to allow mosques prayers in 70 cache = ./cache/cord-315059-l6guql8q.txt txt = ./txt/cord-315059-l6guql8q.txt === reduce.pl bib === id = cord-315860-9j667c03 author = Jullien, Sophie title = Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study date = 2020-04-10 pages = extension = .txt mime = text/plain words = 5633 sentences = 300 flesch = 45 summary = METHODS: This prospective study enrolled children aged 2–59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital with World Health Organization (WHO)-defined clinical pneumonia. CONCLUSION: Respiratory viral infections predominated among this cohort of WHO-defined clinical pneumonia cases, whereas bacterial aetiologies were uncommon, highlighting the epidemiologic transition that Bhutan seems to have reached. We conducted this prospective hospital-based observational study to describe the epidemiology, aetiology, and clinical and radiological presentation of World Health Organization (WHO)defined pneumonia among children aged between 2 and 59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital in Thimphu. All children aged 2-59 months hospitalized with WHO-defined pneumonia (irrespective of severity) were eligible for recruitment (World Health Organization, 2014) (see Box 1). Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study cache = ./cache/cord-315860-9j667c03.txt txt = ./txt/cord-315860-9j667c03.txt === reduce.pl bib === id = cord-284652-7npya3yx author = Shim, Eunha title = Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020 date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3735 sentences = 172 flesch = 55 summary = Results At the regional level, Seoul and Gyeonggi Province have experienced the first peak of COVID-19 in early March, followed by the second wave in early June, withRt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. Therefore, since 10 July, the government banned churches from organizing small gatherings other than regular worship services (KCDC, 2020a To estimate the regional and temporal variability in the reproduction number of COVID-19 in South Korea, including the second wave concentrated in the greater Seoul areas, we analysed the spatiotemporal progression of the epidemic in the country from mid-February to mid-July 2020. In this report, we estimated the doubling time and the effective reproduction number involving two epidemic waves of the COVID-19 epidemic in South Korea by employing the time series of cases by date of symptoms onset for the four most affected Korean regions: Seoul, Gyeonggi Province, Gyeongbuk Province, and Daegu. cache = ./cache/cord-284652-7npya3yx.txt txt = ./txt/cord-284652-7npya3yx.txt === reduce.pl bib === id = cord-317624-qdzhncs0 author = Choi, Min Joo title = Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study date = 2020-10-27 pages = extension = .txt mime = text/plain words = 4287 sentences = 228 flesch = 49 summary = METHODS: Nationwide retrospective case-control study was conducted to compare the effect of HCQ and LPV/r on viral shedding duration among patients with mild-to-moderate COVID-19 using the reimbursement data of National Health Insurance Service. This study aimed to compare the effect of HCQ and LPV/r on the viral shedding duration among patients with mild-to-moderate COVID-19 cases using South Korea's National Health J o u r n a l P r e -p r o o f Insurance Service (NHIS) database. Among these, only mild-to-moderate grade 1 patients were included in the analysis, and the effect of LPV/r or HCQ use on viral shedding duration was evaluated ( Figure 1 ). In the previous studies including mild COVID-19 patients in CTCs, the mean viral shedding duration from symptom onset was 21-24.5 days, which is longer than the results of our control group , Noh et al., 2020 . cache = ./cache/cord-317624-qdzhncs0.txt txt = ./txt/cord-317624-qdzhncs0.txt === reduce.pl bib === id = cord-316505-tdlj5smv author = Kumar, Abhai title = Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers date = 2013-11-28 pages = extension = .txt mime = text/plain words = 4494 sentences = 256 flesch = 50 summary = METHODS: Proteomics-based studies were done to determine the expression of differentially expressed proteins in the plasma of controls, acute typhoid cases, and chronic typhoid carriers. Two-dimensional (2D) gel electrophoresis and mass spectrometry techniques were used to identify newer proteins that may provide an insight into the host-pathogen interactions after Salmonella infection and in further colonization of the host leading to the chronic typhoid carrier state. The expression of proprotein convertase subtilisin, haptoglobin, and albumin in chronic typhoid carriers was significantly higher compared to those of control and acute typhoid cases (p < 0.01 and p < 0.01, respectively; Figure 3 ). typhi infection in enteric fever cases using bacteriological and serological methods and used 2D gel electrophoresis and mass spectrometry as an alternative method to differentiate chronic typhoid carriers based on alterations in the expression of proteins. When analyzed, the plasma proteome of controls, acute typhoid cases, and chronic typhoid carriers showed significant differences in the expression of four protein spots. cache = ./cache/cord-316505-tdlj5smv.txt txt = ./txt/cord-316505-tdlj5smv.txt === reduce.pl bib === id = cord-317399-693q80xo author = Al Wahaibi, Adil title = COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3649 sentences = 218 flesch = 58 summary = title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population In this study, we will analyse the dynamics of COVID-19 infection transmissibility in Oman in the different populations (Omani and non-Omani) and the effects of the introduction of the nonpharmaceutical measures on disease transmissibility. With the increasing numbers of COVID-19 cases in Oman, our study showed the feasibility of using the time-varying Rt to assess and explain transmissibility dynamics and epidemic progression. However, the use of timevarying Rt in assessing the transmissibility dynamics and epidemic progression was a crucial tool to know how the mitigation measures influenced Rt. Nevertheless, a study from China demonstrated that changes in reporting rates substantially affect estimates of Rt. 23 Thus, the initial Rt is influenced by testing frequency, contact tracing, and reporting of mild cases outside hospital. cache = ./cache/cord-317399-693q80xo.txt txt = ./txt/cord-317399-693q80xo.txt === reduce.pl bib === id = cord-317500-ufo2qgj4 author = Scialpi, Michele title = Pulmonary thromboembolism in criticall ill COVID-19 patients date = 2020-04-24 pages = extension = .txt mime = text/plain words = 428 sentences = 37 flesch = 48 summary = Dear Editor, the outbreak of novel Coronavirus disease 2019 in the city of Wuhan, Hubei province of China, has been declared a pandemic by the World Health Organization (WHO) on March 21 st , and has since then forced the scientific community to consider two fundamental aspects: first off, SARS-CoV-2 does not only cause pneumonia and second, the death of many critical ill patients is caused by multiple organ failure (involving the heart, liver, kidneys, blood and immune system). A novel coronavirus from patients with pneumonia in China Acute pulmonary embolism and COVID-19 pneumonia: a random association? COVID-19 Complicated by Acute Pulmonary Embolism Radiology: Cardiothoracic Imaging Findings of Acute Pulmonary Embolism in COVID-19 Patients Management strategy of novel coronavirus (COVID-19) pneumonia in the radiology department: a Chinese experience The Authors declare no conflicts of interest associated for the manuscript entiltled "Pulmonary thromboembolism in criticall ill COVID-19 patients cache = ./cache/cord-317500-ufo2qgj4.txt txt = ./txt/cord-317500-ufo2qgj4.txt === reduce.pl bib === id = cord-311654-ixn65hxb author = Zumla, Alimuddin title = COVID-19 and the scaled-down 2020 Hajj Pilgrimage - Decisive, logical and prudent decision making by Saudi authorities overcomes pre-Hajj public health concerns date = 2020-08-08 pages = extension = .txt mime = text/plain words = 1417 sentences = 74 flesch = 54 summary = Apart from generic prevention and control issues of public health and lockdown measures to limit epidemic spread, specific issues of Mass Gathering (MG) sporting and religious events came under specific spotlight (Alzahrani et al, 2020; Baloch et al, 2020; McCloskey et al, 2020; . WHO with global MG partners, developed comprehensive key recommendations for COVID-19, and since end of February, 2020, there was a stepwise increase in cancellation, temporary suspension or postponement of international and national religious, sporting, musical, and other MGs, as countries worldwide took public health and other measures (WHO, 2020b; McCloskey et al, 2020; Petersen, McCloskey et al, 2020) . The successful completion of the 2020 Hajj is a major tribute to the leadership and commitment of the Saudi authorities, and it reflects their extensive experience of organising the annual Hajj pilgrimage, and continued commitment to improvement public health issues related to mass gatherings events. cache = ./cache/cord-311654-ixn65hxb.txt txt = ./txt/cord-311654-ixn65hxb.txt === reduce.pl bib === id = cord-316209-juvmabdq author = Rutayisire, Erigene title = What works and what does not work in response to COVID-19 prevention and control in Africa date = 2020-06-12 pages = extension = .txt mime = text/plain words = 2335 sentences = 112 flesch = 54 summary = The lower number of COVID-19 cases in most African countries is attributed to inadequate health systems, low-to-absent testing capacity, poor reporting system and insufficient number of medical staff. On 11 March 2020, the World Health Organization (WHO) had declared COVID-19 a pandemic, pointing to the over 118,000 cases of the coronavirus illnesses in over 110 countries and territories around the world and the sustained risk of further global spread. Africa Centers for Diseases Control and Prevention (Africa CDC), World Health Organization and other international agencies are providing support and guidance to many African countries in response to COVID-19 pandemic. Despite reported low case-fatality of COVID-19, the pandemic is likely to cause more deaths in Africa if the compliance to COVID-19 prevention and control measures continues to be ignored as observed in some African countries. cache = ./cache/cord-316209-juvmabdq.txt txt = ./txt/cord-316209-juvmabdq.txt === reduce.pl bib === id = cord-317080-kn56oov6 author = Quadri, Sayed. A. title = COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens date = 2020-05-07 pages = extension = .txt mime = text/plain words = 289 sentences = 31 flesch = 59 summary = title: COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens Gathering of large number of people in close approximation could be a fertile ground for the spread of novel pathogens. COVID 19 is spread through droplet and basic reproduction rate, a 23 measure of transmissibility of the virus, ranges from 2.24 to 3.58 (Zhao et al., 2020) . Public 24 gatherings will evidently increase transmission and therefore social distancing was touted as the 25 foremost preventive strategy.  Suspension of communal gatherings must be promptly done as a preventive strategy 196 whenever novel pathogens emerge, in order to contain its spread.  An international regime of containment measures with regards to suspension of religious 198 congregations during infectious disease outbreaks must be devised. Preliminary estimation of the basic reproduction number of novel 185 coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the 186 early phase of the outbreak cache = ./cache/cord-317080-kn56oov6.txt txt = ./txt/cord-317080-kn56oov6.txt === reduce.pl bib === id = cord-317910-rwhwo55z author = Aziz, Asma B. title = Integrated control of COVID-19 in resource poor countries date = 2020-09-09 pages = extension = .txt mime = text/plain words = 2435 sentences = 129 flesch = 49 summary = In this editorial we discuss several important strategies for controlling COVID-19 including: vaccination, molecular and serological diagnostics, hygiene and WaSH interventions, and low-cost therapeutics. For example, at the beginning of COVID-19 pandemic Bangladesh had only one RT-qPCR laboratory at the Institute of Epidemiology and Disease Control Research (IEDCR) designated for diagnosis of COVID-19 infection for the whole country (170 million) but now there are 77 RT-PCR labs ( Figure 2 ) conducting approximately 20,000 daily tests [9] . As part of a 'district/ward strategy' an Early Warning Surveillance System may be deployed using: rapid diagnostic testing (e.g., Roche antibody test for suspected COVID cases) at health facilities and local hospitals; periodic testing of sewage systems for the presence of SARS-CoV-2 in municipality sewage water; Android-based phone reporting of real-time test results; GIS risk mapping of patients' addresses. cache = ./cache/cord-317910-rwhwo55z.txt txt = ./txt/cord-317910-rwhwo55z.txt === reduce.pl bib === id = cord-318315-r6wqywwe author = Memish, Ziad A. title = Etiology of severe community-acquired pneumonia during the 2013 Hajj—part of the MERS-CoV surveillance program date = 2014-06-23 pages = extension = .txt mime = text/plain words = 3090 sentences = 195 flesch = 51 summary = We aimed to screen Hajj pilgrims admitted to healthcare facilities in 2013 with severe community-acquired pneumonia (CAP) for MERS-CoV and to determine other etiologies. METHODS: Sputum samples were collected from all pilgrims admitted to 15 healthcare facilities in the cities of Makkah and Medina, Saudi Arabia, who were diagnosed with severe CAP on admission, presenting with bilateral pneumonia. 7, 10 In recent years, the Middle East respiratory syndrome coronavirus (MERS-CoV) has also emerged as a cause of serious illness including severe pneumonia. Respiratory tract infections are common illnesses during the Hajj, 15 and pneumonia is the leading cause of hospital admission, including admission to the ICU, during the pilgrimage. 16 In the current study, as part of the Saudi MoH MERS-CoV surveillance, we investigated the etiology of severe CAP in pilgrims attending the 2013 Hajj requiring hospitalization. 7,10 Studies performed during previous Hajj seasons have reported the organism as a cause of respiratory tract infections including penumonia. cache = ./cache/cord-318315-r6wqywwe.txt txt = ./txt/cord-318315-r6wqywwe.txt === reduce.pl bib === id = cord-318808-1cfwj5uq author = Li, Ying title = Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years date = 2020-06-12 pages = extension = .txt mime = text/plain words = 1656 sentences = 111 flesch = 55 summary = title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years Abstract Background Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. Therefore, the aim of this study was to compare the different clinical Page 5 of 15 J o u r n a l P r e -p r o o f 5 presentations between patients with infected with COVID-19 pneumonia versus influenza A pneumonia, to provide some recommendations for their differential diagnosis. Our present study revealed that COVID-19 manifested as mild, severe pneumonia were less than influenza A patients. In conclusion, COVID-19 patients were mild not only in clinical symptoms but also in laboratory examinations which including lymphocyte, CRP, PCT, D-dimer in the children under 5 years. cache = ./cache/cord-318808-1cfwj5uq.txt txt = ./txt/cord-318808-1cfwj5uq.txt === reduce.pl bib === id = cord-319814-tyqb473m author = Zhang, Dingmei title = Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date = 2014-06-11 pages = extension = .txt mime = text/plain words = 3480 sentences = 208 flesch = 51 summary = METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. cache = ./cache/cord-319814-tyqb473m.txt txt = ./txt/cord-319814-tyqb473m.txt === reduce.pl bib === id = cord-320860-qt84oicg author = Zhang, Aining title = Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date = 2020-09-15 pages = extension = .txt mime = text/plain words = 2359 sentences = 131 flesch = 47 summary = title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis cache = ./cache/cord-320860-qt84oicg.txt txt = ./txt/cord-320860-qt84oicg.txt === reduce.pl bib === id = cord-324231-nik7xizn author = Aitsi-Selmi, Amina title = Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction date = 2016-04-07 pages = extension = .txt mime = text/plain words = 2882 sentences = 127 flesch = 39 summary = The following actions with a public health focus are agreed in the Sendai Framework with local, national, regional, and global partners as relevant: ''Enhancing the resilience of national health systems through training and capacity development; strengthening the design and implementation of inclusive policies and social safety-net mechanisms, including access to basic health care services towards the eradication of poverty; finding durable solutions in the post-disaster phase to empower and assist people disproportionately affected by disasters, including those with life-threatening and chronic disease; enhancing cooperation between health authorities and other relevant stakeholders to strengthen country capacity for disaster risk management for health; the implementation of the International Health Regulations (2005) and the building of resilient health systems; improving the resilience of new and existing critical infrastructure, including hospitals, to ensure that they remain safe, effective and operational during and after disasters, to provide live-saving and essential services; establishing a mechanism of case registry and a database of mortality caused by disaster to improve the prevention of morbidity and mortality and enhancing recovery schemes to provide psychosocial support and mental health services for all people in need''. cache = ./cache/cord-324231-nik7xizn.txt txt = ./txt/cord-324231-nik7xizn.txt === reduce.pl bib === id = cord-320902-1hfxju5f author = Filocamo, Giovanni title = Use of anakinra in severe COVID-19: a case report date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1440 sentences = 88 flesch = 46 summary = As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still's disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient's critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). cache = ./cache/cord-320902-1hfxju5f.txt txt = ./txt/cord-320902-1hfxju5f.txt === reduce.pl bib === id = cord-323455-26xi2lqf author = AlBarrak, Ali title = Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date = 2018-02-21 pages = extension = .txt mime = text/plain words = 4237 sentences = 201 flesch = 49 summary = This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. pneumoniae among adult Hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with Hajj and inform vaccination policy-making. General pattern of community-acquired pneumonia (CAP) case admissions to hospitals during the study period. It was aimed to systematically enroll all hospitalized X-ray-confirmed CAP cases among Hajj pilgrims during the study period. cache = ./cache/cord-323455-26xi2lqf.txt txt = ./txt/cord-323455-26xi2lqf.txt === reduce.pl bib === id = cord-318181-xxc7vdnt author = Ahmed, Anwar E. title = Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date = 2018-03-14 pages = extension = .txt mime = text/plain words = 4387 sentences = 201 flesch = 50 summary = A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient's clinical status, 'yes/no', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). cache = ./cache/cord-318181-xxc7vdnt.txt txt = ./txt/cord-318181-xxc7vdnt.txt === reduce.pl bib === id = cord-323696-0lq8ql6n author = Bearman, Gonzalo title = Reflections on the COVID-19 Pandemic in the USA: Will We Better Prepared Next Time? date = 2020-05-20 pages = extension = .txt mime = text/plain words = 1856 sentences = 134 flesch = 51 summary = We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. 1 We reflect on the US and its response to the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. cache = ./cache/cord-323696-0lq8ql6n.txt txt = ./txt/cord-323696-0lq8ql6n.txt === reduce.pl bib === id = cord-320785-42p8292o author = Lobo, Andréa de Paula title = COVID-19 epidemic in Brazil: where we at? date = 2020-06-16 pages = extension = .txt mime = text/plain words = 682 sentences = 55 flesch = 70 summary = Abstract Objetive to analyze the trends of COVID-19 in Brazil in 2020 by Federal Units (FU). Joinpoint regression models were applied to identify points of inflection in COVID-19 trends, considering the days since the 50th confirmed case as time unit. Conclusions In summary, our results show that all FUs in Brazil present upward trends of COVID-19. Discussion: Although all FUs presented upward trends in the number of cumulative cases of COVID-19, 18 out of 27 FUs showed a reduction in the pace of the trend in the last segment. Even though the FUs from the Southeast region presented most of the confirmed cases, the highest ADPC values were found in the Northeast and North regions. (36.9;58.8) 3-11 13.8*(12.7;14.9) 11-20 8.1*(7.2;9.0 • All of Federative Units in Brazil shows a upward in accumulated cases of COVID-19. • Each Federative Unit in Brazil is at a different stage of the COVID-19 pandemic. cache = ./cache/cord-320785-42p8292o.txt txt = ./txt/cord-320785-42p8292o.txt === reduce.pl bib === id = cord-320829-uepneyug author = He, Zhongping title = Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date = 2005-08-10 pages = extension = .txt mime = text/plain words = 2631 sentences = 138 flesch = 59 summary = title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS cache = ./cache/cord-320829-uepneyug.txt txt = ./txt/cord-320829-uepneyug.txt === reduce.pl bib === id = cord-330819-vfagxsdz author = Althouse, Benjamin M title = Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date = 2018-08-14 pages = extension = .txt mime = text/plain words = 4662 sentences = 239 flesch = 44 summary = Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. cache = ./cache/cord-330819-vfagxsdz.txt txt = ./txt/cord-330819-vfagxsdz.txt === reduce.pl bib === id = cord-326881-3j2e92dj author = Vassallo, M. title = Patients with Covid-19 exhibit different immunological profiles according to their clinical presentation date = 2020-09-28 pages = extension = .txt mime = text/plain words = 2385 sentences = 132 flesch = 45 summary = Conclusions In a population of elderly patients recently infected with Covid-19, CD10 + B cell levels were inversely correlated with clinical severity. However, clinical expression of Covid-19 is extremely variable, with, in some cases, asymptomatic or mild forms [15] , while in other subjects severe forms culminating in acute respiratory distress syndrome (ARDS) have been described, requiring patients to be transferred to Intensive Care Units. The aim of this study was to retrospectively analyze the immunological profile of patients at early stages of Covid-19 in order to identify potential risk factors for subsequent clinical deterioration. We conducted an observational, retrospective cohort study on patients admitted to the Internal Medicine and Infectious Diseases Department in Cannes General Hospital, from March to May 2020, with confirmed Covid-19 infection. In a population of elderly patients at a very early stage of Covid-19, we found that levels of CD10+ B lymphocyte cells were predictive of the clinical severity. cache = ./cache/cord-326881-3j2e92dj.txt txt = ./txt/cord-326881-3j2e92dj.txt === reduce.pl bib === id = cord-330136-o8df8szx author = Fan, Hua title = Cardiac injuries in patients with coronavirus disease 2019: Not to be ignored date = 2020-05-11 pages = extension = .txt mime = text/plain words = 2167 sentences = 133 flesch = 54 summary = 40 non-survivors had test result of hs-TnI，they were divided into two groups based on cardiac injury，Further analysis revealed that non-survivors with elevated hs-TnI levels on admission had shorter duration from symptom onset to death, and TnI elevation was related to the dismal prognosis. The mortality of critically ill COVID-19 patients is high, but its mechanism is not clear at present, and it might be related to the virus-induced acute lung injury, inflammatory factor storm. Our study discovered that the level of hs-TnI increased in many patients on admission, indicating that cardiac injury occurred in the early stage of the disease.The incidence rate of cardiac injury among patients at admission was 16.44%, with the non-survivors having an incidence rate of as high as 25.53%. Association of Cardiac Injury With Mortality in Hospitalized Patients With COVID-19 in Wuhan, China cache = ./cache/cord-330136-o8df8szx.txt txt = ./txt/cord-330136-o8df8szx.txt === reduce.pl bib === id = cord-328459-nmd81sue author = Dioscoridi, Lorenzo title = Covid-19 exposure risk for family members of healthcare workers: an observational study date = 2020-07-04 pages = extension = .txt mime = text/plain words = 1243 sentences = 78 flesch = 60 summary = However, no available papers discussed the risk of exposure of family members (FM) of HWs. Aims The present study collected the data of SARS-COV-2 positive FM of HWs using serological rapid IgM/IgG tests (SRT) compared with positive HWs at SRT and serological quantitative IgG test (SQT). The key element of our study was to assess the total number of family members (FM) of HWs positive to SARS-COV-2 infection and the number of positive HWs working in a COVID-19 hospital. The SRT studied both IgG and IgM with a declared sensitivity of 100% for IgG and 85% for IgM SQT used in the study was ELISA test researching IgG anti-S1/anti-S2 for SARS-CoV-2, available and validated for HWs screening in the region of the study (Lombardia, Italy). For both HWs and FMs, exposure to COVID-19 cases, onset of suspicious symptoms (also before the study period since the 1 st February 2020), photos of the serological tests after 10 minutes, serological tests' platforms, past medical history, drugs and clinical course were registered. cache = ./cache/cord-328459-nmd81sue.txt txt = ./txt/cord-328459-nmd81sue.txt === reduce.pl bib === id = cord-336954-rh88lod0 author = Shim, Eunha title = Transmission potential and severity of COVID-19 in South Korea date = 2020-03-18 pages = extension = .txt mime = text/plain words = 2972 sentences = 154 flesch = 55 summary = OBJECTIVES: Since the first case of 2019 novel coronavirus (COVID-19) identified on Jan 20, 2020 in South Korea, the number of cases rapidly increased, resulting in 6,284 cases including 42 deaths as of March 6, 2020. However, the number of confirmed cases of SARS-CoV-2 infection started to increase rapidly on February 19, 2020 with a total of 6,284 confirmed COVID-19 cases including 42 deaths reported as of March 6, 2020 according to the Korea Centers for Disease Control and Prevention (KCDC) (KCDC, 2020) ( Table 1 ). Under the empirical reporting delay distribution from early Korean cases with available dates of onset, the intrinsic growth rate (r) was estimated at 0.6 (95% CI: 0.6, 0.7) and the scaling of growth parameter (p) was estimated at 0.8 (95% CI: 0.7, 0.8), indicating sub-exponential growth dynamics of COVID-19 cache = ./cache/cord-336954-rh88lod0.txt txt = ./txt/cord-336954-rh88lod0.txt === reduce.pl bib === id = cord-339576-0d6sa9pe author = Guallar, María Pilar title = Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1380 sentences = 79 flesch = 56 summary = Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure cache = ./cache/cord-339576-0d6sa9pe.txt txt = ./txt/cord-339576-0d6sa9pe.txt === reduce.pl bib === id = cord-338225-8dlxnpcn author = De Meyer, Sandra title = Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date = 2020-05-29 pages = extension = .txt mime = text/plain words = 329 sentences = 27 flesch = 60 summary = Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. cache = ./cache/cord-338225-8dlxnpcn.txt txt = ./txt/cord-338225-8dlxnpcn.txt === reduce.pl bib === id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 pages = extension = .txt mime = text/plain words = 1791 sentences = 101 flesch = 41 summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave's disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. cache = ./cache/cord-334603-yt2pmxi3.txt txt = ./txt/cord-334603-yt2pmxi3.txt === reduce.pl bib === id = cord-340992-88t1c0zs author = Nikolai, Lea A title = Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3092 sentences = 193 flesch = 44 summary = Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection cache = ./cache/cord-340992-88t1c0zs.txt txt = ./txt/cord-340992-88t1c0zs.txt === reduce.pl bib === id = cord-326143-6ndqgxy8 author = Wang, Qiang title = Successful recovery of severe COVID-19 with cytokine storm treating with extracorporeal blood purification date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1325 sentences = 89 flesch = 59 summary = COVID-19 associated cytokine storm could induce ARDS rapidly and the patients would require the support of mechanic ventilation. We present a case of severe SARS-CoV-2 infection who recovered from cytokine storm. The patients with confirmed COVID-19 progressed to acute respiratory distress syndrome (ARDS) rapidly in an incident rate as high as 41.8% 1 , and many of them require mechanic ventilation. Cytokines could be eliminated effectively by extracorporeal blood purification (EBP) 4 , which thus could interrupt the initiation and progression of inflammation cascade in the scenario of COVID-19. IL-6 (198.66 pg/ml) was almost 10 folds of normal range (≤5.9 pg/ml) which indicated an initiation of cytokine storm on day 12 ( Figure 1 ). The patient was largely stable until the chest distress exacerbated and blood in phlegm developed on day 14. Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease cache = ./cache/cord-326143-6ndqgxy8.txt txt = ./txt/cord-326143-6ndqgxy8.txt === reduce.pl bib === id = cord-338576-gh1plurq author = Regen, Francesca title = A Simple Approach to Optimum Pool Size for Pooled SARS-CoV-2 Testing date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1201 sentences = 69 flesch = 54 summary = Finally, we derive a simple-to-use formula and table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. Here we provide a simple strategy to estimate the optimum pool size for a two-staged pooling based on a known target prevalence. The optimum pool size for a given frequency is defined by the local minima of the isolines in figure 1A and can be more precisely determined by the first derivative of equation 1 Results from our analysis clearly demonstrate the relation between target prevalence rates and optimum pool sizes in a two staged pooling strategy. The relation between the estimated analyses per specimen and a pool size are given for various target prevalence rates as defined by equation 1 (isolines; A). Local minima suggest optimum pool sizes at the respective target prevalence rate (isolines; A). cache = ./cache/cord-338576-gh1plurq.txt txt = ./txt/cord-338576-gh1plurq.txt === reduce.pl bib === id = cord-325325-xw7627x9 author = Skeik, Nedaa title = Influenza viruses and the evolution of avian influenza virus H5N1 date = 2007-10-02 pages = extension = .txt mime = text/plain words = 4079 sentences = 254 flesch = 51 summary = While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. cache = ./cache/cord-325325-xw7627x9.txt txt = ./txt/cord-325325-xw7627x9.txt === reduce.pl bib === id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3770 sentences = 212 flesch = 51 summary = Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . cache = ./cache/cord-324295-9c1zxjng.txt txt = ./txt/cord-324295-9c1zxjng.txt === reduce.pl bib === id = cord-340279-bq5owwot author = Espíndola, Otávio de Melo title = Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date = 2020-06-04 pages = extension = .txt mime = text/plain words = 285 sentences = 37 flesch = 52 summary = key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection cache = ./cache/cord-340279-bq5owwot.txt txt = ./txt/cord-340279-bq5owwot.txt === reduce.pl bib === id = cord-341775-mucatzaa author = Shafi, Shuja title = The annual Hajj pilgrimage—minimizing the risk of ill health in pilgrims from Europe and opportunity for driving the best prevention and health promotion guidelines date = 2016-06-22 pages = extension = .txt mime = text/plain words = 2252 sentences = 124 flesch = 50 summary = Mass gathering sporting and religious events pose important public health challenges, including the transmission of infectious diseases, exacerbation of non-communicable diseases, and disorders related to climate change. [1] [2] [3] [4] [5] Every year, the Kingdom of Saudi Arabia (KSA) hosts the Hajj pilgrimage, which is the largest mass gathering in the world held on a recurrent annual basis. Mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. cache = ./cache/cord-341775-mucatzaa.txt txt = ./txt/cord-341775-mucatzaa.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-332348-yi85sfks author = Liang, Yujie title = Neurosensory dysfunction: a diagnostic marker of early COVID-19 date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2748 sentences = 172 flesch = 56 summary = Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. cache = ./cache/cord-332348-yi85sfks.txt txt = ./txt/cord-332348-yi85sfks.txt === reduce.pl bib === === reduce.pl bib === id = cord-345275-h0hvaxgx author = Sun, Mengyao title = Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date = 2020-07-04 pages = extension = .txt mime = text/plain words = 5308 sentences = 286 flesch = 56 summary = title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection cache = ./cache/cord-345275-h0hvaxgx.txt txt = ./txt/cord-345275-h0hvaxgx.txt === reduce.pl bib === id = cord-344478-5gp7v1uh author = Rosenberg, Eli S. title = Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 date = 2020-07-29 pages = extension = .txt mime = text/plain words = 760 sentences = 56 flesch = 53 summary = title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 The study from Arshad et al on the use of hydroxychloroquine, with and without azithromycin, for the treatment of inpatients with COVID-19 in one healthcare system (Henry Ford Health System) is a new entrant into the rapidly expanding literature on the treatment of this disease [1, 2] . Treatment with Hydroxychloroquine, Azithromycin, and Combination in Patients Hospitalized with COVID-19 Observational Study of Hydroxychloroquine in Hospitalized Patients with Covid-19 Association of Treatment With Hydroxychloroquine or Azithromycin With In-Hospital Mortality in Patients With COVID-19 in Treatment with Hydroxychloroquine Cut Death Rate Significantly in COVID-19 Patients, Henry Ford Health System Study Shows cache = ./cache/cord-344478-5gp7v1uh.txt txt = ./txt/cord-344478-5gp7v1uh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === ===== Reducing email addresses cord-306200-d5qn65k0 cord-293942-n5ypkftc cord-315059-l6guql8q cord-340410-s9haq8y1 Creating transaction Updating adr table ===== Reducing keywords cord-257073-dm80bxnd cord-029882-kufs0fxe cord-255901-nl9k8uwd cord-268389-0agwvsrv cord-262017-utvy0i8l cord-258881-74aijckl cord-274845-pqvlh3eg cord-258669-ubw6mdzi cord-282360-byqhzyzi cord-283590-xvnv17zy cord-282177-8l7zukg4 cord-262310-z0m6uuzf cord-272179-wvw5mmy3 cord-268037-szhzmzys cord-268883-nf4fm7r7 cord-272015-1anph6qi cord-259501-iggw1exl cord-254872-w6d397js cord-280627-dfnc9g2c cord-275866-m89hgf41 cord-268599-z54p3dk3 cord-266253-oyid5haj cord-254776-m4makxr8 cord-024631-yvek5vjz cord-297396-r1p7xn3a cord-008219-ng9xb46c cord-258078-k7y8k1vx cord-276254-q04hqra2 cord-253102-z15j8izi cord-290100-wnjjqqn5 cord-257200-q0vqlerz cord-279976-juz9jnfk cord-291638-oatrjbo3 cord-254377-j8e8gb0l cord-301079-n1nytr6k cord-278406-n5e3a09i cord-300583-0krbrj4w cord-260518-mswb3q67 cord-279581-d2l4nnex cord-292988-q1yz9y8k cord-280060-gzby85u9 cord-288167-976qxja2 cord-255021-acgfwjwi cord-258250-zueo1xfa cord-297715-qcwp2jdv cord-283812-ocfjj79v cord-305788-z75yv88e cord-308080-1heu9vuv cord-271495-5906wju4 cord-290206-fmy4zrim cord-265146-j0n3a4m6 cord-303417-1237ykxt cord-306682-01q775up cord-261672-0cresfn8 cord-275250-ilmgy7ce cord-261058-yu2qw02l cord-274230-old0xmcc cord-274028-dvsvtsn0 cord-275191-lgze4zex cord-305782-gnzwe2z2 cord-260332-tnz6k2z1 cord-289304-9srk0ohb cord-304743-0bsdahh6 cord-311413-uiwjrvru cord-257737-obadq502 cord-311026-mpr3xb2a cord-292092-o6s5nw49 cord-311479-8pjoz64q cord-282421-yialyuav cord-304872-hnxmtbrf cord-311453-l6quzef6 cord-276445-m5vjo3ym cord-306200-d5qn65k0 cord-293942-n5ypkftc cord-308114-68cgub5o cord-310691-6danlh8h cord-293630-zc8huo1j cord-259837-5tbdqzxr cord-279892-37vyazby cord-283891-m36un1y2 cord-287209-hkrarxsd cord-286743-z0e5arlm cord-297829-aynigoud cord-291367-rtmsrh16 cord-273961-ja8xggnd cord-300774-5mrkmctl cord-305763-160heazx cord-315860-9j667c03 cord-292256-jp80u828 cord-257265-lkzytud0 cord-315059-l6guql8q cord-284652-7npya3yx cord-302409-40ktyt5q cord-316505-tdlj5smv cord-317624-qdzhncs0 cord-317500-ufo2qgj4 cord-311654-ixn65hxb cord-317399-693q80xo cord-316209-juvmabdq cord-317080-kn56oov6 cord-318315-r6wqywwe cord-317910-rwhwo55z cord-319814-tyqb473m cord-318808-1cfwj5uq cord-320860-qt84oicg cord-293247-ltxt2dfv cord-309032-idjdzs97 cord-320829-uepneyug cord-301085-tk2vvxj7 cord-320902-1hfxju5f cord-273090-fdzkfo1u cord-277640-vy7ex5lv cord-318181-xxc7vdnt cord-324231-nik7xizn cord-323455-26xi2lqf cord-330819-vfagxsdz cord-323696-0lq8ql6n cord-330136-o8df8szx cord-326881-3j2e92dj cord-339576-0d6sa9pe cord-328459-nmd81sue cord-325325-xw7627x9 cord-324295-9c1zxjng cord-338576-gh1plurq cord-330692-rqwkkfp0 cord-326143-6ndqgxy8 cord-341775-mucatzaa cord-343789-6tq0kcfd cord-320785-42p8292o cord-334603-yt2pmxi3 cord-332348-yi85sfks cord-344478-5gp7v1uh cord-345275-h0hvaxgx cord-336954-rh88lod0 cord-340410-s9haq8y1 cord-346461-eqyte6ko cord-351740-779g8tr1 cord-355343-dtdsd8j2 cord-347349-caz5fwl1 cord-349645-6o8773c5 cord-354780-yzyixucr cord-323332-vu2cre8k cord-347907-0nrejsgr cord-355480-mx9dbm73 cord-349418-98sgr5iv cord-356074-kw8c2fgk cord-347499-7q47jh14 cord-321412-6g3obmzc cord-340992-88t1c0zs cord-340279-bq5owwot cord-338225-8dlxnpcn Creating transaction Updating wrd table ===== Reducing urls cord-255901-nl9k8uwd cord-259501-iggw1exl cord-268389-0agwvsrv cord-262310-z0m6uuzf cord-280627-dfnc9g2c cord-290100-wnjjqqn5 cord-291638-oatrjbo3 cord-258250-zueo1xfa cord-292988-q1yz9y8k cord-305788-z75yv88e cord-308080-1heu9vuv cord-265146-j0n3a4m6 cord-274230-old0xmcc cord-273961-ja8xggnd cord-311413-uiwjrvru cord-257265-lkzytud0 cord-315860-9j667c03 cord-305763-160heazx cord-292256-jp80u828 cord-324231-nik7xizn cord-334603-yt2pmxi3 cord-330819-vfagxsdz cord-347349-caz5fwl1 cord-318181-xxc7vdnt cord-319814-tyqb473m Creating transaction Updating url table ===== Reducing named entities cord-257073-dm80bxnd cord-029882-kufs0fxe cord-268389-0agwvsrv cord-255901-nl9k8uwd cord-258669-ubw6mdzi cord-274845-pqvlh3eg cord-282360-byqhzyzi cord-283590-xvnv17zy cord-262310-z0m6uuzf cord-272015-1anph6qi cord-262017-utvy0i8l cord-259501-iggw1exl cord-258881-74aijckl cord-276254-q04hqra2 cord-282177-8l7zukg4 cord-254872-w6d397js cord-268037-szhzmzys cord-254776-m4makxr8 cord-268883-nf4fm7r7 cord-257200-q0vqlerz cord-266253-oyid5haj cord-258078-k7y8k1vx cord-272179-wvw5mmy3 cord-275866-m89hgf41 cord-275250-ilmgy7ce cord-297396-r1p7xn3a cord-254377-j8e8gb0l cord-290100-wnjjqqn5 cord-288167-976qxja2 cord-268599-z54p3dk3 cord-008219-ng9xb46c cord-280627-dfnc9g2c cord-297715-qcwp2jdv cord-279581-d2l4nnex cord-280060-gzby85u9 cord-258250-zueo1xfa cord-255021-acgfwjwi cord-261058-yu2qw02l cord-308080-1heu9vuv cord-024631-yvek5vjz cord-292988-q1yz9y8k cord-291638-oatrjbo3 cord-279976-juz9jnfk cord-301079-n1nytr6k cord-260518-mswb3q67 cord-283812-ocfjj79v cord-278406-n5e3a09i cord-300583-0krbrj4w cord-265146-j0n3a4m6 cord-305788-z75yv88e cord-290206-fmy4zrim cord-271495-5906wju4 cord-274230-old0xmcc cord-275191-lgze4zex cord-274028-dvsvtsn0 cord-306682-01q775up cord-303417-1237ykxt cord-305782-gnzwe2z2 cord-260332-tnz6k2z1 cord-311413-uiwjrvru cord-311026-mpr3xb2a cord-304743-0bsdahh6 cord-292092-o6s5nw49 cord-289304-9srk0ohb cord-282421-yialyuav cord-257737-obadq502 cord-259837-5tbdqzxr cord-304872-hnxmtbrf cord-253102-z15j8izi cord-311453-l6quzef6 cord-293942-n5ypkftc cord-306200-d5qn65k0 cord-277640-vy7ex5lv cord-273090-fdzkfo1u cord-308114-68cgub5o cord-293630-zc8huo1j cord-257265-lkzytud0 cord-273961-ja8xggnd cord-297829-aynigoud cord-279892-37vyazby cord-283891-m36un1y2 cord-291367-rtmsrh16 cord-301085-tk2vvxj7 cord-309032-idjdzs97 cord-286743-z0e5arlm cord-305763-160heazx cord-300774-5mrkmctl cord-287209-hkrarxsd cord-276445-m5vjo3ym cord-293247-ltxt2dfv cord-292256-jp80u828 cord-315059-l6guql8q cord-284652-7npya3yx cord-315860-9j667c03 cord-317399-693q80xo cord-316505-tdlj5smv cord-317624-qdzhncs0 cord-311654-ixn65hxb cord-317080-kn56oov6 cord-316209-juvmabdq cord-318808-1cfwj5uq cord-317910-rwhwo55z cord-318315-r6wqywwe cord-317500-ufo2qgj4 cord-320860-qt84oicg cord-319814-tyqb473m cord-302409-40ktyt5q cord-318181-xxc7vdnt cord-320902-1hfxju5f cord-324231-nik7xizn cord-320785-42p8292o cord-261672-0cresfn8 cord-311479-8pjoz64q cord-323455-26xi2lqf cord-310691-6danlh8h cord-330819-vfagxsdz cord-323696-0lq8ql6n cord-320829-uepneyug cord-326881-3j2e92dj cord-334603-yt2pmxi3 cord-328459-nmd81sue cord-330136-o8df8szx cord-336954-rh88lod0 cord-339576-0d6sa9pe cord-338225-8dlxnpcn cord-340992-88t1c0zs cord-326143-6ndqgxy8 cord-338576-gh1plurq cord-325325-xw7627x9 cord-324295-9c1zxjng cord-340279-bq5owwot cord-330692-rqwkkfp0 cord-343789-6tq0kcfd cord-341775-mucatzaa cord-332348-yi85sfks cord-346461-eqyte6ko cord-344478-5gp7v1uh cord-345275-h0hvaxgx cord-351740-779g8tr1 cord-355343-dtdsd8j2 cord-349418-98sgr5iv cord-347349-caz5fwl1 cord-356074-kw8c2fgk cord-354780-yzyixucr cord-349645-6o8773c5 cord-340410-s9haq8y1 cord-355480-mx9dbm73 cord-347499-7q47jh14 cord-321412-6g3obmzc cord-323332-vu2cre8k cord-347907-0nrejsgr Creating transaction Updating ent table ===== Reducing parts of speech cord-029882-kufs0fxe cord-257073-dm80bxnd cord-255901-nl9k8uwd cord-259501-iggw1exl cord-258669-ubw6mdzi cord-282360-byqhzyzi cord-262017-utvy0i8l cord-262310-z0m6uuzf cord-274845-pqvlh3eg cord-258881-74aijckl cord-258078-k7y8k1vx cord-282177-8l7zukg4 cord-272179-wvw5mmy3 cord-268389-0agwvsrv cord-275866-m89hgf41 cord-283590-xvnv17zy cord-268599-z54p3dk3 cord-268037-szhzmzys cord-276254-q04hqra2 cord-268883-nf4fm7r7 cord-254872-w6d397js cord-253102-z15j8izi cord-280627-dfnc9g2c cord-272015-1anph6qi cord-266253-oyid5haj cord-254776-m4makxr8 cord-297396-r1p7xn3a cord-257200-q0vqlerz cord-008219-ng9xb46c cord-024631-yvek5vjz cord-290100-wnjjqqn5 cord-275250-ilmgy7ce cord-291638-oatrjbo3 cord-279976-juz9jnfk cord-254377-j8e8gb0l cord-288167-976qxja2 cord-297715-qcwp2jdv cord-255021-acgfwjwi cord-258250-zueo1xfa cord-280060-gzby85u9 cord-292988-q1yz9y8k cord-261058-yu2qw02l cord-279581-d2l4nnex cord-308080-1heu9vuv cord-283812-ocfjj79v cord-278406-n5e3a09i cord-305788-z75yv88e cord-260518-mswb3q67 cord-300583-0krbrj4w cord-301079-n1nytr6k cord-306682-01q775up cord-290206-fmy4zrim cord-303417-1237ykxt cord-265146-j0n3a4m6 cord-274230-old0xmcc cord-271495-5906wju4 cord-261672-0cresfn8 cord-305782-gnzwe2z2 cord-275191-lgze4zex cord-274028-dvsvtsn0 cord-260332-tnz6k2z1 cord-304743-0bsdahh6 cord-289304-9srk0ohb cord-257737-obadq502 cord-311026-mpr3xb2a cord-292092-o6s5nw49 cord-311479-8pjoz64q cord-259837-5tbdqzxr cord-282421-yialyuav cord-311413-uiwjrvru cord-304872-hnxmtbrf cord-276445-m5vjo3ym cord-306200-d5qn65k0 cord-293630-zc8huo1j cord-311453-l6quzef6 cord-293942-n5ypkftc cord-273090-fdzkfo1u cord-308114-68cgub5o cord-257265-lkzytud0 cord-310691-6danlh8h cord-301085-tk2vvxj7 cord-277640-vy7ex5lv cord-279892-37vyazby cord-283891-m36un1y2 cord-291367-rtmsrh16 cord-286743-z0e5arlm cord-287209-hkrarxsd cord-297829-aynigoud cord-300774-5mrkmctl cord-273961-ja8xggnd cord-305763-160heazx cord-309032-idjdzs97 cord-293247-ltxt2dfv cord-292256-jp80u828 cord-302409-40ktyt5q cord-315059-l6guql8q cord-317399-693q80xo cord-315860-9j667c03 cord-284652-7npya3yx cord-316505-tdlj5smv cord-311654-ixn65hxb cord-317624-qdzhncs0 cord-317500-ufo2qgj4 cord-316209-juvmabdq cord-317080-kn56oov6 cord-317910-rwhwo55z cord-318315-r6wqywwe cord-318808-1cfwj5uq cord-320860-qt84oicg cord-320902-1hfxju5f cord-320785-42p8292o cord-319814-tyqb473m cord-338225-8dlxnpcn cord-323455-26xi2lqf cord-328459-nmd81sue cord-324231-nik7xizn cord-323696-0lq8ql6n cord-330136-o8df8szx cord-339576-0d6sa9pe cord-340992-88t1c0zs cord-320829-uepneyug cord-330819-vfagxsdz cord-336954-rh88lod0 cord-326143-6ndqgxy8 cord-338576-gh1plurq cord-324295-9c1zxjng cord-340279-bq5owwot cord-346461-eqyte6ko cord-326881-3j2e92dj cord-343789-6tq0kcfd cord-341775-mucatzaa cord-318181-xxc7vdnt cord-344478-5gp7v1uh cord-351740-779g8tr1 cord-340410-s9haq8y1 cord-355343-dtdsd8j2 cord-323332-vu2cre8k cord-345275-h0hvaxgx cord-347349-caz5fwl1 cord-349645-6o8773c5 cord-355480-mx9dbm73 cord-330692-rqwkkfp0 cord-332348-yi85sfks cord-347907-0nrejsgr cord-349418-98sgr5iv cord-321412-6g3obmzc cord-354780-yzyixucr cord-334603-yt2pmxi3 cord-356074-kw8c2fgk cord-347499-7q47jh14 cord-325325-xw7627x9 Creating transaction Updating pos table Building ./etc/reader.txt cord-308114-68cgub5o cord-275191-lgze4zex cord-317624-qdzhncs0 cord-260518-mswb3q67 cord-291367-rtmsrh16 cord-318181-xxc7vdnt number of items: 151 sum of words: 323,439 average size in words: 2,431 average readability score: 51 nouns: patients; study; cases; infection; disease; health; virus; influenza; coronavirus; data; risk; infections; time; case; pneumonia; transmission; studies; outbreak; treatment; days; countries; epidemic; children; number; syndrome; results; analysis; group; control; pandemic; rate; measures; age; hospital; symptoms; care; mortality; population; years; diseases; viruses; fever; laboratory; patient; test; authors; detection; -p; samples; use verbs: used; including; reported; shown; associated; infect; increase; based; found; detect; confirmed; comparing; identified; done; develop; following; required; causing; receiving; provided; reduces; considering; indicate; suggest; collected; performed; treated; estimated; presenting; emerging; related; tested; given; occur; conducted; observed; taking; needs; declare; leading; remains; hospitalized; determine; assessed; spread; makes; known; described; according; resulted adjectives: respiratory; clinical; severe; viral; covid-19; acute; high; positive; human; first; higher; public; infectious; novel; asymptomatic; different; significant; early; non; medical; negative; new; low; global; effective; common; lower; many; potential; important; available; specific; standard; similar; mild; local; primary; key; general; several; previous; large; international; likely; possible; inflammatory; epidemiological; critical; multiple; second adverbs: also; however; well; significantly; respectively; therefore; even; still; especially; particularly; moreover; rapidly; worldwide; recently; highly; critically; furthermore; currently; first; less; already; previously; least; often; yet; approximately; now; statistically; mainly; generally; relatively; prior; later; newly; far; much; usually; early; potentially; similarly; finally; specifically; daily; together; likely; almost; subsequently; clearly; alone; initially pronouns: we; it; our; their; they; its; he; them; i; she; his; us; her; themselves; you; one; itself; your; ours; yourself; www.cdc.gov/flu; ws; theirs; ourselves; oneself; my; igm/; em proper nouns: SARS; COVID-19; CoV-2; China; MERS; J; Hajj; CoV; Health; Wuhan; PCR; Coronavirus; Africa; Korea; East; Middle; March; Disease; RT; Ebola; South; RNA; HIV; World; Dis; Int; Table; January; February; Saudi; Organization; H1N1; Kawasaki; ICU; April; A; Arabia; Hubei; Rt; sha; RSV; Hospital; S.; CT; CI; May; H5N1; TCZ; Kong; EV71 keywords: covid-19; sars; mers; patient; hajj; china; case; respiratory; korea; health; ebola; africa; virus; rna; pcr; influenza; hiv; east; wuhan; tcz; taiwan; study; rsv; middle; measure; hubei; hcq; h1n1; gathering; day; cov-2; child; asymptomatic; zambia; vp1; viral; vaccine; uganda; trends; travel; tpe; tocilizumab; test; swab; staphylococcus; standard; srt; southeast; south; sendai one topic; one dimension: covid file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388893/ titles(s): The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials three topics; one dimension: patients; health; infection file(s): https://api.elsevier.com/content/article/pii/S120197121300338X, https://www.ncbi.nlm.nih.gov/pubmed/32360552/, https://www.ncbi.nlm.nih.gov/pubmed/15936970/ titles(s): Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers | COVID-19–We urgently need to start developing an exit strategy | Kawasaki disease: What is the epidemiology telling us about the etiology? five topics; three dimensions: patients covid sars; health cases covid; patients respiratory covid; covid patients study; disease human infection file(s): https://www.sciencedirect.com/science/article/pii/S1201971220302332, https://doi.org/10.1016/j.ijid.2013.01.002, https://doi.org/10.1016/j.ijid.2016.04.020, https://api.elsevier.com/content/article/pii/S1201971220306093, https://www.ncbi.nlm.nih.gov/pubmed/15936970/ titles(s): Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study | Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan | Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() | Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab | Kawasaki disease: What is the epidemiology telling us about the etiology? Type: cord title: journal-intJInfectDis-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Int J Infect Dis" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-279581-d2l4nnex author: Abuhabib, A.A. title: Unique situation of Gaza Strip dealing with COVID-19 crisis date: 2020-09-03 words: 1153.0 sentences: 47.0 pages: flesch: 45.0 cache: ./cache/cord-279581-d2l4nnex.txt txt: ./txt/cord-279581-d2l4nnex.txt summary: Constructively, this study follows direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario within a limited time frame covering the period from 22 March to 05 July 2020. This study follows the direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario likelihood determination and consequences identification within a limited time frame covering the period from 22 March to 05 July 2020. abstract: Infected COVID19 cases continue to increase, having already reached 21 million globally, attracting scientists around the world to trying to find a possible vaccine. Unlike many places around the world, movement restrictions and difficulties in travelling in and out due to 13 years old blockade with no possibility for tourists to travel in, has benefited Gaza in terms of being self-isolated and less likely to have many travellers or foreigners carrying the virus and infecting the population. First cases discovered on 22 March 2020 and by 05 July 2020, they were still only 72 cases confirmed, 60 of whom successfully treated, 11 active cases and only 1 death. Constructively, this study follows direct observation approach with in-depth disk review for data collected locally from official sources (Governmental bodies, UN agencies, and INGOs), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with COVID19 supported by the application of simple risk matrix for each scenario within a limited time frame covering the period from 22 March to 05 July 2020. Three different risk scenarios associated with COVID19 risks studied and analysed towards understanding exceptional circumstances surrounding Gaza along with potential mitigation measures executed and suggested. url: https://www.ncbi.nlm.nih.gov/pubmed/32891733/ doi: 10.1016/j.ijid.2020.08.070 id: cord-308114-68cgub5o author: Afrin, Lawrence B. title: Covid-19 Hyperinflammation and Post-Covid-19 Illness May Be Rooted in Mast Cell Activation Syndrome date: 2020-09-10 words: 3455.0 sentences: 186.0 pages: flesch: 45.0 cache: ./cache/cord-308114-68cgub5o.txt txt: ./txt/cord-308114-68cgub5o.txt summary: MCs, present in all vascularized tissues but dominantly at the environmental interfaces and in vessel walls (Akin and Metcalfe, 2004) , are activated by the SARS-Cov-2 coronavirus which causes Covid-19 infection (Kritas et al., 2020; Theoharides, 2020; Zhou et al., 2020) , leading to MC activation and resulting release of various subsets of the MC''s >1000 potent multi-action mediators (Ibelgaufts, 2020) (including biogenic amines (e.g., histamine), proteases (e.g., tryptase and chymase), cytokines (e.g., interleukins and TNF-α), eicosanoids (e.g., prostaglandins and leukotrienes), heparin, and growth factors) increasingly thought to play a key role in driving the hyperinflammation of severe Covid-19 illness (Kempuraj et al., 2020; Valent et al., 2020) . abstract: Objectives One-fifth of Covid-19 patients suffer a severely symptomatic, hyperinflammatory course, but specific causes remain unclear. Mast cells (MCs) are activated by SARS-CoV-2. Though only recently recognized, MC activation syndrome (MCAS), usually due to acquired MC clonality, is a chronic multisystem disorder with inflammatory and allergic themes and estimated prevalence of 17%. We describe a novel conjecture explaining how MCAS might cause propensity for severe acute Covid-19 infection and chronic post-Covid-19 illnesses. Methods Observations of Covid-19 illness in patients with/without MCAS, set against our extensive clinical experience with MCAS. Results The prevalence of MCAS is concordant with the prevalence of severe cases within the Covid-19-infected population. Much of Covid-19’s hyperinflammation is concordant with manners of inflammation which MC activation can drive. Drugs with activity against MCs or their mediators have been preliminarily observed helpful in Covid-19 patients. None of our treated MCAS patients who have endured Covid-19 infection have suffered severe courses of the infection, let alone mortality. Conclusions Hyperinflammatory cytokine storms in many severely symptomatic Covid-19 patients may be rooted in aberrant response to SARS-CoV-2 by the dysfunctional MCs of MCAS rather than normal response by normal MCs. If provable, our conjecture has significant therapeutic and prognostic implications. url: https://www.ncbi.nlm.nih.gov/pubmed/32920235/ doi: 10.1016/j.ijid.2020.09.016 id: cord-305788-z75yv88e author: Agergaard, Charlotte Nielsen title: Challenging diagnostics in familial transmission from asymptomatic COVID-19 carrier. Should we group SARS-CoV-2 samples from households? date: 2020-09-28 words: 727.0 sentences: 64.0 pages: flesch: 61.0 cache: ./cache/cord-305788-z75yv88e.txt txt: ./txt/cord-305788-z75yv88e.txt summary: Few days after returning to Denmark, six travel companions developed symptoms of COVID-19 and were tested SARS-CoV-2 PCR positive. Extension of the national COVID-19 testing April 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested SARS-CoV-2 PCR positive. Comparative testing with the SARS-CoV-2 S1/S2 IgG assay (CLIA, DiaSorin, Liaison) found the index-person and three daughters positive and the wife just below cut-off (Table 1) . This family cluster incorporates several aspects of the challenges surrounding COVID-19 and SARS-CoV-2 diagnostics. The familial transmission from an asymptomatic carrier who displayed a positive SARS-CoV-2 PCR four weeks after infestation and a subsequent immunologic response. The wife and three daughters, who J o u r n a l P r e -p r o o f had mild symptoms of COVID-19, presented diverse and divergent SARS-CoV-2 PCR results, yet displayed an immunologic response. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220321585?v=s5 doi: 10.1016/j.ijid.2020.09.1442 id: cord-318181-xxc7vdnt author: Ahmed, Anwar E. title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia date: 2018-03-14 words: 4387.0 sentences: 201.0 pages: flesch: 50.0 cache: ./cache/cord-318181-xxc7vdnt.txt txt: ./txt/cord-318181-xxc7vdnt.txt summary: A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient''s clinical status, ''yes/no'', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). abstract: BACKGROUND: The rapid and accurate identification of individuals who are at high risk of Middle East respiratory syndrome coronavirus (MERS-CoV) infection remains a major challenge for the medical and scientific communities. The aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia. METHODS: A two-center, retrospective case–control study was performed. A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. According to the rRT-PCR results, 135 patients were positive for MERS-CoV and 225 were negative. Demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject. RESULTS: A risk prediction model to identify pneumonia patients at increased risk of MERS-CoV was developed. The model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (WBC) count, low alanine aminotransferase (ALT), and high aspartate aminotransferase (AST). The model performed well in predicting MERS-CoV infection (area under the receiver operating characteristics curves (AUC) 0.8162), on internal validation (AUC 0.8037), and on a goodness-of-fit test (p = 0.592). The risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783. CONCLUSIONS: This study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of MERS-CoV infection. This risk prediction model could be useful for the early identification of patients at the highest risk of MERS-CoV infection. Further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/29550445/ doi: 10.1016/j.ijid.2018.03.005 id: cord-324231-nik7xizn author: Aitsi-Selmi, Amina title: Reducing risks to health and wellbeing at mass gatherings: the role of the Sendai Framework for Disaster Risk Reduction date: 2016-04-07 words: 2882.0 sentences: 127.0 pages: flesch: 39.0 cache: ./cache/cord-324231-nik7xizn.txt txt: ./txt/cord-324231-nik7xizn.txt summary: The following actions with a public health focus are agreed in the Sendai Framework with local, national, regional, and global partners as relevant: ''''Enhancing the resilience of national health systems through training and capacity development; strengthening the design and implementation of inclusive policies and social safety-net mechanisms, including access to basic health care services towards the eradication of poverty; finding durable solutions in the post-disaster phase to empower and assist people disproportionately affected by disasters, including those with life-threatening and chronic disease; enhancing cooperation between health authorities and other relevant stakeholders to strengthen country capacity for disaster risk management for health; the implementation of the International Health Regulations (2005) and the building of resilient health systems; improving the resilience of new and existing critical infrastructure, including hospitals, to ensure that they remain safe, effective and operational during and after disasters, to provide live-saving and essential services; establishing a mechanism of case registry and a database of mortality caused by disaster to improve the prevention of morbidity and mortality and enhancing recovery schemes to provide psychosocial support and mental health services for all people in need''''. abstract: Mass gatherings of people at religious pilgrimages and sporting events are linked to numerous health hazards, including the transmission of infectious diseases, physical injuries, and an impact on local and global health systems and services. As with other forms of disaster, mass gathering-related disasters are the product of the management of different hazards, levels of exposure, and vulnerability of the population and environment, and require comprehensive risk management that looks beyond single hazards and response. Incorporating an all-hazard, prevention-driven, evidence-based approach that is multisectoral and multidisciplinary is strongly advocated by the Sendai Framework for Disaster Risk Reduction 2015–2030. This paper reviews some of the broader impacts of mass gatherings, the opportunity for concerted action across policy sectors and scientific disciplines offered by the year 2015 (including through the Sendai Framework), and the elements of a 21(st) century approach to mass gatherings. url: https://api.elsevier.com/content/article/pii/S1201971216310190 doi: 10.1016/j.ijid.2016.04.006 id: cord-257073-dm80bxnd author: Akmatov, Manas K. title: E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date: 2011-08-17 words: 3515.0 sentences: 177.0 pages: flesch: 46.0 cache: ./cache/cord-257073-dm80bxnd.txt txt: ./txt/cord-257073-dm80bxnd.txt summary: OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. abstract: OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. METHODS: The study was conducted among a convenience sample of employees (n = 53) at a research institution (December 2009–April 2010). Real-time data on the occurrence of acute respiratory symptoms and a nasal self-swab were collected prospectively, with automated weekly e-mails as a reminder mechanism. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect respiratory viral pathogens in the swabs. RESULTS: Fifty-one out of 53 participants completed the study. The study design was well accepted. Thirty (∼57%) participants reported at least one episode of acute respiratory infection and returned the nasal swab during the study period (eight participants reported two episodes). The majority had no difficulties taking the self-swab and preferred this to swabbing by study personnel. Most participants obtained and returned the swabs within the recommended time. Viral respiratory pathogens were detected in 19 of 38 swabs (50%), with coronaviruses 229E/NL63 and OC43 and rhinoviruses A and B constituting 17 positive swabs (89%). CONCLUSIONS: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. url: https://api.elsevier.com/content/article/pii/S120197121100155X doi: 10.1016/j.ijid.2011.07.005 id: cord-317399-693q80xo author: Al Wahaibi, Adil title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date: 2020-08-20 words: 3649.0 sentences: 218.0 pages: flesch: 58.0 cache: ./cache/cord-317399-693q80xo.txt txt: ./txt/cord-317399-693q80xo.txt summary: title: COVID-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population In this study, we will analyse the dynamics of COVID-19 infection transmissibility in Oman in the different populations (Omani and non-Omani) and the effects of the introduction of the nonpharmaceutical measures on disease transmissibility. With the increasing numbers of COVID-19 cases in Oman, our study showed the feasibility of using the time-varying Rt to assess and explain transmissibility dynamics and epidemic progression. However, the use of timevarying Rt in assessing the transmissibility dynamics and epidemic progression was a crucial tool to know how the mitigation measures influenced Rt. Nevertheless, a study from China demonstrated that changes in reporting rates substantially affect estimates of Rt. 23 Thus, the initial Rt is influenced by testing frequency, contact tracing, and reporting of mild cases outside hospital. abstract: BACKGROUND: COVID-19’s emergence carries with it many uncertainties and challenges, one of which is epidemic management strategies. Oman has implemented non-pharmaceutical interventions (NPIs) to mitigate the impact of COVID-19. However, responses to NPIs may be different across different populations in a country with a large number of migrants like Oman. This study investigates the different responses to NPIs assessing the use of time-varying reproduction number (R(t)) to monitor it. METHODS: Polymerase chain reaction (PCR) laboratory-confirmed COVID-19 data from Oman was used from February 24th to June 3rd, 2020 and included demographic and epidemiological information. Data were arranged into pairs of infector–infectee, and two main libraries of R software were used to estimate reproductive number (R(t)). R(t) was calculated for both Omanis and non-Omanis. FINDINGS: A total of 13,538 cases were included, 44·9% of which were Omanis. Among all, we identified 2769 infector–infectee pairs to calculate R(t). There was a sharp drop in R(t) from 3·7, (95% confidence interval [CI] 2·8-4·6) mid-March to 1·4 (95% CI 1·2–1·7) in late March in response to NPIs. Then R(t) decreased to 1·2 (95% CI 1·1–1·3) late April when it rose, corresponding to the easing up of NPIs. Comparing the two groups, the response to major public health controls was more evident in Omanis in reducing the R(t) to 1·09 (95% CI 0·84–1·3) at the end of March. INTERPRETATION: Use of real-time estimation of R(t) has allowed us to follow the effect of NPIs. The migrant population responds differently than the Omani population. url: https://www.sciencedirect.com/science/article/pii/S1201971220306688?v=s5 doi: 10.1016/j.ijid.2020.08.039 id: cord-266253-oyid5haj author: Al-Abaidani, I.S. title: Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman date: 2014-10-29 words: 1108.0 sentences: 57.0 pages: flesch: 53.0 cache: ./cache/cord-266253-oyid5haj.txt txt: ./txt/cord-266253-oyid5haj.txt summary: Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. abstract: Several countries in the Middle East and around 22 countries worldwide have reported cases of human infection with the Middle East respiratory syndrome coronavirus (MERS-CoV). The exceptionally high fatality rate resulting from MERS-CoV infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. url: https://www.sciencedirect.com/science/article/pii/S1201971214016488 doi: 10.1016/j.ijid.2014.10.003 id: cord-275191-lgze4zex author: Al-Sadeq, Duaa W. title: The incidence of the novel coronavirus SARS-CoV-2 among asymptomatic patients: a systematic review date: 2020-07-02 words: 3287.0 sentences: 221.0 pages: flesch: 48.0 cache: ./cache/cord-275191-lgze4zex.txt txt: ./txt/cord-275191-lgze4zex.txt summary: AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. The following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the COVID-19 infection in asymptomatic patients, and (iii) articles published in English or at least with an abstract in English. No exclusion criteria were followed unless the studies did not report the incidence of SARS-CoV-2 in asymptomatic patients, published in a non-English language, or do not have full-text access. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. abstract: BACKGROUND: the recent outbreak of the coronavirus disease 2019 (COVID‐19) has quickly spread globally since its discovery in Wuhan, China, in December 2019. A comprehensive strategy, including surveillance, diagnostics, research, and clinical treatment is urgently needed to win the battle against COVID-19. Recently, numerous studies reported the incidence of SARS-CoV-2 in asymptomatic patients. Yet, the incidence and viral transmission from the asymptomatic cases are not apparent yet. AIM: this study aims to systematically review the published literature on SARS-CoV-2 in the asymptomatic patients to estimate the incidence of COVID-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. METHOD: the literature was searched through four scientific databases: PubMed, Web of Science, Scopus, and Science Direct. RESULTS: a total of 63 studies satisfied the inclusion criteria where the majority of the reported studies were from China. However, there was a lack of SARS-CoV-2 epidemiological studies from several countries worldwide, tracing the actual incidence of COVID-19, especially in asymptomatic patients. Studies with a large sample size (n>1000) estimated that percentage of people contracting SARS-CoV-2 and are likely to be asymptomatic ranges from 1.2-12.9%. However, the other studies with a smaller sample size reported a much higher incidence and indicated that up to 87.9% of COVID-19 infected individuals could be asymptomatic. Most of these studies indicated that asymptopatics are a potential source of infection to the community. CONCLUSION: this review highlighted the need for more robust and well-designed studies to better estimate COVID-19 incidence among asymptomatic patients worldwide. The early identification of the asymptomatic cases, as well as monitoring and tracing close contact, could help in mitigating the spread of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305336?v=s5 doi: 10.1016/j.ijid.2020.06.098 id: cord-343789-6tq0kcfd author: Al-Tawfiq, Jaffar A. title: Ribavirin and interferon therapy in patients infected with the Middle East respiratory syndrome coronavirus: an observational study date: 2014-01-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) has been reported to have a high case-fatality rate. Currently, there is no specific therapy or vaccine with proven effectiveness for MERS-CoV infections. METHODS: A combination of ribavirin and interferon therapy was used for the treatment of five MERS-CoV-positive patients. We reviewed the therapeutic schedule and the outcome of these patients. RESULTS: All patients were critically ill with acute respiratory distress syndrome treated with adjunctive corticosteroids and were on mechanical ventilation at the time of initiation of therapy. The median time from admission to therapy with ribavirin and interferon was 19 (range 10–22) days. None of the patients responded to the supportive or therapeutic interventions and all died of their illness. CONCLUSIONS: While ribavirin and interferon may be effective in some patients, our practical experience suggests that critically ill patients with multiple comorbidities who are diagnosed late in the course of their illness may not benefit from combination antiviral therapy as preclinical data suggest. There is clearly an urgent need for a novel effective antiviral therapy for this emerging global threat. url: https://www.sciencedirect.com/science/article/pii/S1201971213003767 doi: 10.1016/j.ijid.2013.12.003 id: cord-323455-26xi2lqf author: AlBarrak, Ali title: Proportion of adult community-acquired pneumonia cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016 date: 2018-02-21 words: 4237.0 sentences: 201.0 pages: flesch: 49.0 cache: ./cache/cord-323455-26xi2lqf.txt txt: ./txt/cord-323455-26xi2lqf.txt summary: This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. pneumoniae among adult Hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with Hajj and inform vaccination policy-making. General pattern of community-acquired pneumonia (CAP) case admissions to hospitals during the study period. It was aimed to systematically enroll all hospitalized X-ray-confirmed CAP cases among Hajj pilgrims during the study period. abstract: BACKGROUND: The Hajj mass gathering is a risk for pneumococcal disease. This study was performed to evaluate the proportion of adult community-acquired pneumonia (CAP) cases attributable to Streptococcus pneumoniae among Hajj pilgrims in 2016. To add sensitivity to etiological attribution, a urine antigen test was used in addition to culture-based methods. METHODS: Adult subjects hospitalized with X-ray-confirmed CAP were enrolled prospectively from all general hospitals designated to treat Hajj pilgrims in the holy cities of Mecca and Medina. Patients were treated according to local standard of care and administered the BinaxNow S. pneumoniae urine antigen test. RESULTS: From August 23 to September 23, 2016, a total of 266 patients with CAP were enrolled in the study, 70.6% of whom were admitted to hospitals in Mecca; 53% of the cases were admitted after the peak of Hajj. Patients originated from 43 countries. Their mean age was 65.3 years and the male to female ratio was 2:1. Just over 36% of the cases had diabetes, 10% declared that they were smokers, and 45.4% of cases were treated in the intensive care unit (ICU). The overall case-fatality rate was 10.1%, but was higher among those treated in the ICU and in those with invasive disease. The proportion of CAP cases positive for S. pneumoniae, based on culture or urine antigen test, was 18.0% (95% confidence interval 13.9–23.1%). CONCLUSIONS: CAP during Hajj has an important clinical impact. A proportion of CAP cases among Hajj pilgrims were attributable to S. pneumoniae, a pathogen for which vaccines are available. Additional studies to determine the serotypes causing pneumococcal disease could further inform vaccine policy for Hajj pilgrims. url: https://doi.org/10.1016/j.ijid.2018.02.008 doi: 10.1016/j.ijid.2018.02.008 id: cord-282421-yialyuav author: Alcoba-Florez, Julia title: Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection date: 2020-08-01 words: 1049.0 sentences: 69.0 pages: flesch: 55.0 cache: ./cache/cord-282421-yialyuav.txt txt: ./txt/cord-282421-yialyuav.txt summary: In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. 2020) , standard diagnosis continues to rely on RNA extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative PCR (RT-qPCR) that entail one or several primer-probe sets for targeting SARS-CoV-2 sequences . Our results evidenced a wide variability in the sensitivity of RT-qPCR solutions for SARS-CoV-2 detection which associated with a proportion of FN ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting SARS-CoV-2 sensitivity (stage of infection and type of specimen) (Pan et al. abstract: Abstract Objectives The ongoing COVID-19 pandemic continues imposing a demand for diagnostic screening. In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2. Methods We evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. That of best sensitivity was also assessed with direct nasopharyngeal swab viral transmission medium (VTM) heating, overcoming the RNA extraction step. Results We found a wide variability in the sensitivity of RT-qPCR solutions that associated with a range of false negatives from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Direct preheating of VTM combined with the best solution provided a sensitivity of 72.5% (62.5-81.0), in the range of some of the solutions based on standard RNA extractions. Conclusions We evidenced sensitivity limitations of currently used RT-qPCR solutions. Our results will help to calibrate the impact of false negative diagnoses of COVID-19, and to detect and control new SARS-CoV-2 outbreaks and community transmissions. url: https://doi.org/10.1016/j.ijid.2020.07.058 doi: 10.1016/j.ijid.2020.07.058 id: cord-254377-j8e8gb0l author: Ali, Sadaf title: Acute cor pulmonale from saddle pulmonary embolism in a patient with previous Covid-19 – should we prolong prophylactic anticoagulation? date: 2020-06-13 words: 1447.0 sentences: 87.0 pages: flesch: 43.0 cache: ./cache/cord-254377-j8e8gb0l.txt txt: ./txt/cord-254377-j8e8gb0l.txt summary: However, the risk associated with mild and moderate illness from Covid-19 is unknown, and there is no current recommendation for prophylaxis against thromboembolism in patients after hospital treatment unless there are established thrombophilic risk factors. We report the case of a 52-year old woman, who presented with massive saddle pulmonary embolism after one week of initial hospital discharge, successfully thrombolysed that raises the question of consideration of extended prophylactic anticoagulation even in low risk Covid-19 cases. 3 We report a case of acute massive PE successfully managed by thrombolysis in a patient who was discharged after one week of initial hospital treatment for Covid-19 pneumonia which raises serious concerns about the indication for extended prophylactic anticoagulation in such cases. Emerging data and clinical experience suggest an increased prevalence of venous thromboembolic events (VTE) in COVID-19, especially in patients with severe disease requiring hospitalization, and even among those who are not critically ill. abstract: Abstract Severe corona virus disease 19 (Covid-19) is known to be associated with exaggerated risk of thromboembolism. However, the risk associated with mild and moderate illness from Covid-19 is unknown, and there is no current recommendation for prophylaxis against thromboembolism in patients after hospital treatment unless there are established thrombophilic risk factors. We report the case of a 52-year old woman, who presented with massive saddle pulmonary embolism after one week of initial hospital discharge, successfully thrombolysed that raises the question of consideration of extended prophylactic anticoagulation even in low risk Covid-19 cases. url: https://api.elsevier.com/content/article/pii/S1201971220304744 doi: 10.1016/j.ijid.2020.06.039 id: cord-347907-0nrejsgr author: Alqahtani, Amani S. title: Exploring barriers to and facilitators of preventive measures against infectious diseases among Australian Hajj pilgrims: cross-sectional studies before and after Hajj date: 2016-02-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: For reasons that have yet to be elucidated, the uptake of preventive measures against infectious diseases by Hajj pilgrims is variable. The aim of this study was to identify the preventive advice and interventions received by Australian pilgrims before Hajj, and the barriers to and facilitators of their use during Hajj. METHODS: Two cross-sectional surveys of Australians pilgrims aged ≥18 years were undertaken, one before and one after the Hajj 2014. RESULTS: Of 356 pilgrims who completed the survey (response rate 94%), 80% had the influenza vaccine, 30% the pneumococcal vaccine, and 30% the pertussis vaccine. Concern about contracting disease at Hajj was the most cited reason for vaccination (73.4%), and not being aware of vaccine availability was the main reason for non-receipt (56%). Those who obtained pre-travel advice were twice as likely to be vaccinated as those who did not seek advice. Of 150 pilgrims surveyed upon return, 94% reported practicing hand hygiene during Hajj, citing ease of use (67%) and belief in its effectiveness (62.4%) as the main reasons for compliance; university education was a significant predictor of hand hygiene adherence. Fifty-three percent used facemasks, with breathing discomfort (76%) and a feeling of suffocation (40%) being the main obstacles to compliance. CONCLUSION: This study indicates that there are significant opportunities to improve awareness among Australian Hajj pilgrims about the importance of using preventive health measures. url: https://doi.org/10.1016/j.ijid.2016.02.005 doi: 10.1016/j.ijid.2016.02.005 id: cord-024631-yvek5vjz author: Althaus, T. title: Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 words: 4327.0 sentences: 226.0 pages: flesch: 43.0 cache: ./cache/cord-024631-yvek5vjz.txt txt: ./txt/cord-024631-yvek5vjz.txt summary: OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. In this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in Southeast Asia, and to evaluate the performance of CRP for discriminating between bacteria and viruses. Specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of C-reactive protein (CRP) testing on antibiotic prescription in primary care [38] . We investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of CRP in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. Investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. abstract: OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. METHODS: Blood and nasopharyngeal swab specimens were taken from children and adults with fever (>37.5˚C) or history of fever (<14 days) in Thailand and Myanmar. RESULTS: Of 773 patients with at least one blood or nasopharyngeal swab specimen collected, 227 (29.4%) had a target organism detected. Influenza virus type A was detected in 85/227 cases (37.5%), followed by dengue virus (30 cases, 13.2%), respiratory syncytial virus (24 cases, 10.6%) and Leptospira spp. (9 cases, 4.0%). Clinical outcome was similar between patients with a bacterial or a viral organism, regardless of antibiotic prescription. CRP was higher among patients with a bacterial organism compared to those with a viral organism (median 18 mg/L, interquartile range [10-49] versus 10 mg/L [≤8-22], p-value 0.003), with an area under the curve of 0.65, 95% confidence interval (0.55-0.75). CONCLUSIONS: Serious bacterial infections requiring antibiotics are exceptions rather than the rule in the first lines of care. CRP-testing could assist in ruling out such cases in settings where diagnostic uncertainty is high and routine antibiotic prescription is common. The original CRP randomised-controlled trial (RCT) was registered with ClinicalTrials.gov, number NCT02758821. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211754/ doi: 10.1016/j.ijid.2020.05.016 id: cord-330819-vfagxsdz author: Althouse, Benjamin M title: Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date: 2018-08-14 words: 4662.0 sentences: 239.0 pages: flesch: 44.0 cache: ./cache/cord-330819-vfagxsdz.txt txt: ./txt/cord-330819-vfagxsdz.txt summary: Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. abstract: BACKGROUND: Acute respiratory infections (ARIs) are the most common causes of death in children under 5 years of age. While the etiology of most pneumonia and ARI episodes is undiagnosed, a broad range of ARI-causing viruses circulate widely in South East Asia. However, the patterns and drivers of the seasonal transmission dynamics are largely unknown. Here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for ARIs in Nha Trang, Vietnam. METHODS: Hospital based enhanced surveillance of childhood ARI is ongoing at Khanh Hoa General Hospital in Nha Trang. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. Seasonal patterns of childhood ARI hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. RESULTS: Respiratory syncytial virus peaks in the late summer months, and influenza A in April to June. We find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. Using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. CONCLUSIONS: Our results are important for understanding the temporal risk associated with circulating pathogens in Southern Central Vietnam. Specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region. url: https://doi.org/10.1016/j.ijid.2018.08.001 doi: 10.1016/j.ijid.2018.08.001 id: cord-301085-tk2vvxj7 author: Askarian, Mehrdad title: Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran date: 2006-07-11 words: 2610.0 sentences: 137.0 pages: flesch: 42.0 cache: ./cache/cord-301085-tk2vvxj7.txt txt: ./txt/cord-301085-tk2vvxj7.txt summary: title: Knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of Shiraz, Iran Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Objective: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. Method: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. [2] [3] [4] The purpose of our study was to measure the level of knowledge, attitude, and practice in surgeons and physicians in Shiraz University of Medical Sciences affiliated hospitals. abstract: OBJECTIVE: To measure levels of knowledge, attitudes, and practice toward standard precautions (SP) in medical practitioners of Shiraz University of Medical Sciences affiliated hospitals in Iran. METHOD: In this cross-sectional study, knowledge, attitude, and practice related to SP among four medical staff groups – surgeons, surgical residents, physicians and medical residents – were assessed using a questionnaire. RESULTS: Across the four medical staffing groups the median levels of knowledge ranged from 6 to 7 (maximum score 9), median attitude scores were high ranging from 35 to 36 (maximum score 45), while median practice scores were low, ranging from 2 to 3 (maximum score 9). A moderate relationship between knowledge and attitudes was found in surgical residents and medical residents (r = 0.397, p = 0.030 and r = 0.554, p = 0.006, respectively). No significant correlation was found between knowledge and practice between the groups. A significant but poor (r = 0.399, p = 0.029) relationship between attitude and practice was found in surgical residents. CONCLUSION: Specific training programs may have to target newly graduated medical practitioners to establish acceptance of appropriate practices that will enable them to adopt and adhere to SP while their older counterparts may require more intense continuous assistance. url: https://www.ncbi.nlm.nih.gov/pubmed/16837226/ doi: 10.1016/j.ijid.2006.01.006 id: cord-317910-rwhwo55z author: Aziz, Asma B. title: Integrated control of COVID-19 in resource poor countries date: 2020-09-09 words: 2435.0 sentences: 129.0 pages: flesch: 49.0 cache: ./cache/cord-317910-rwhwo55z.txt txt: ./txt/cord-317910-rwhwo55z.txt summary: In this editorial we discuss several important strategies for controlling COVID-19 including: vaccination, molecular and serological diagnostics, hygiene and WaSH interventions, and low-cost therapeutics. For example, at the beginning of COVID-19 pandemic Bangladesh had only one RT-qPCR laboratory at the Institute of Epidemiology and Disease Control Research (IEDCR) designated for diagnosis of COVID-19 infection for the whole country (170 million) but now there are 77 RT-PCR labs ( Figure 2 ) conducting approximately 20,000 daily tests [9] . As part of a ''district/ward strategy'' an Early Warning Surveillance System may be deployed using: rapid diagnostic testing (e.g., Roche antibody test for suspected COVID cases) at health facilities and local hospitals; periodic testing of sewage systems for the presence of SARS-CoV-2 in municipality sewage water; Android-based phone reporting of real-time test results; GIS risk mapping of patients'' addresses. abstract: Low and middle income countries (LMICs) face many challenges in controlling COVID-19 in their countries. Health-care resources are limited and so are ICU beds. RT-PCR testing is conducted on a limited scale and treatment options are few. There is no vaccine. Therefore, what low cost solutions remain for the prevention, diagnosis, and treatment of SARS-CoV-2? How should these essential health services be delivered in order to reach the most vulnerable in our societies? In this editorial we discuss several important strategies for controlling COVID-19 including: vaccination, molecular and serological diagnostics, hygiene and WaSH interventions, and low-cost therapeutics. We also discuss the delivery of such services in order to reach the most in need. The proposed integrated control strategy requires immediate action and political will in order to reduce the widening health inequalities caused by the pandemic. url: https://doi.org/10.1016/j.ijid.2020.09.009 doi: 10.1016/j.ijid.2020.09.009 id: cord-289304-9srk0ohb author: Bagnato, Sergio title: Critical illness myopathy after COVID-19 date: 2020-08-05 words: 1723.0 sentences: 98.0 pages: flesch: 48.0 cache: ./cache/cord-289304-9srk0ohb.txt txt: ./txt/cord-289304-9srk0ohb.txt summary: We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 (COVID-19). We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 . The patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (EMG) of the proximal and distal muscles, and direct muscle stimulation (DMS). In this report, we describe neurophysiological findings from a patient who developed severe muscular weakness, likely due to CIM, after hospitalization for COVID-19. The patient described here had myopathy, with greater involvement of the proximal muscles in the lower limbs, probably reflecting ICU-acquired weakness. Since rehabilitation programs can be effective to reverse muscle weakness caused by CIM, health systems must plan to provide adequate access to rehabilitative facilities for patients requiring both pulmonary and motor rehabilitative treatment after COVID-19. abstract: We describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (ICU) due to coronavirus disease 2019 (COVID-19). The patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (EMG) of the proximal and distal muscles, and direct muscle stimulation (DMS). Nerve conduction studies showed normal sensory conduction and low-amplitude compound muscle action potentials (CMAPs). EMG revealed signs of myopathy, which were more pronounced in the lower limbs. The post-DMS CMAP was absent in the quadriceps and of reduced amplitude in the tibialis anterior muscle. Based on these clinical and neurophysiological findings, a diagnosis of critical illness myopathy was made according to the current diagnostic criteria. Given the large number of patients with COVID-19 who require long ICU stays, many of these patients are very likely to develop ICU-acquired weakness, as did the patient described here. Health systems must plan to provide adequate access to rehabilitative facilities for both pulmonary and motor rehabilitative treatment after COVID-19. url: https://api.elsevier.com/content/article/pii/S1201971220306068 doi: 10.1016/j.ijid.2020.07.072 id: cord-355480-mx9dbm73 author: Bajunirwe, Francis title: Long distance truck drivers and the increasing risk of COVID-19 spread in Uganda date: 2020-06-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Objectives To examine the patterns of COVID-19 transmission in Uganda. Methods We reviewed press releases from the Uganda Ministry of Health from when the first case was announced on March 22 up to May 29, 2020 a 10-week period. We obtained the press releases from the MoH website and the Twitter handle (@MinofHealthUG). Data include number of persons tested and the categories classified as international arrivals, community members and long distance truck drivers. Results The first cases were international arrivals from Asia and Europe and thereafter community cases emerged. However, in the middle of April 2020, COVID-19 cases were detected among long distance truck drivers. By May 29, 2020, a total of 89, 224 persons had been tested and overall 442 tested positive. Of those that tested positive, majority or 317 (71.8%) were truck drivers, 75 (16.9%) were community cases and 50 (11.3%) were international arrivals. Majority of community cases have been linked to contact with truck drivers. Conclusions The truck drivers are the most frequently diagnosed category, and have become a core group for COVID-19 in Uganda. They have generated significant local transmission which now threatens a full blown epidemic in the country unless strict controls are put in place. url: https://doi.org/10.1016/j.ijid.2020.06.085 doi: 10.1016/j.ijid.2020.06.085 id: cord-255901-nl9k8uwd author: Barasheed, Osamah title: Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date: 2016-03-29 words: 4522.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-255901-nl9k8uwd.txt txt: ./txt/cord-255901-nl9k8uwd.txt summary: Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. abstract: OBJECTIVES: The risk of acquisition and transmission of respiratory infections is high among attendees of mass gatherings (MGs). Currently used interventions have limitations yet the role of facemask in preventing those infections at MG has not been systematically reviewed. We have conducted a systematic review to synthesise evidence about the uptake and effectiveness of facemask against respiratory infections in MGs. METHODS: A comprehensive literature search was conducted according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines using major electronic databases such as, Medline, EMBASE, SCOPUS and CINAHL. RESULTS: Of 25 studies included, the pooled sample size was 12710 participants from 55 countries aged 11 to 89 years, 37% were female. The overall uptake of facemask ranged from 0.02% to 92.8% with an average of about 50%. Only 13 studies examined the effectiveness of facemask, and their pooled estimate revealed significant protectiveness against respiratory infections (relative risk [RR] = 0.89, 95% CI: 0.84-0.94, p < 0.01), but the study end points varied widely. CONCLUSION: A modest proportion of attendees of MGs use facemask, the practice is more widespread among health care workers. Facemask use seems to be beneficial against certain respiratory infections at MGs but its effectiveness against specific infection remains unproven. url: https://api.elsevier.com/content/article/pii/S1201971216310104 doi: 10.1016/j.ijid.2016.03.023 id: cord-323696-0lq8ql6n author: Bearman, Gonzalo title: Reflections on the COVID-19 Pandemic in the USA: Will We Better Prepared Next Time? date: 2020-05-20 words: 1856.0 sentences: 134.0 pages: flesch: 51.0 cache: ./cache/cord-323696-0lq8ql6n.txt txt: ./txt/cord-323696-0lq8ql6n.txt summary: We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. 1 We reflect on the US and its response to the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. abstract: Abstract The United States (US) spends more on healthcare than any other country with little evidence of better, or even comparable, outcomes. We reflect on the US and the COVID-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. These include the US healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of American exceptionalism. Without institutionalizing the lessons learned, the US will be positioned to repeat the missteps of COVID-19 with the next pandemic. url: https://doi.org/10.1016/j.ijid.2020.05.059 doi: 10.1016/j.ijid.2020.05.059 id: cord-271495-5906wju4 author: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 words: 1995.0 sentences: 107.0 pages: flesch: 53.0 cache: ./cache/cord-271495-5906wju4.txt txt: ./txt/cord-271495-5906wju4.txt summary: Data and modelling supported the existence of ''superspreaders'' which played a crucial role in propagating the disease by being very efficient at transmitting SARS-CoV-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (Stein, 2011) . Similarly, early modelling and data suggested that a small proportion of cases of COVID-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for SARS-CoV-2 (MacKenzie D, 2020, Frieden and Lee, 2020). Infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. Therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. abstract: Abstract The current global propagation of COVID-19 is heterogeneous, with slow transmission continuing in many countries, and exponential propagation in others, in which the time that took to begin this explosive spread varies greatly. It is proposed that this could be explained by cascading superspreading events, in which new infections caused by a superspreader are more likely to be highly infectious. The mechanism suggested for this is related to viral loads. Exposure to high viral loads may result in infections of high intensity, which exposes new cases to high viral loads, and so on. This notion is supported by experimental veterinary research. url: https://www.ncbi.nlm.nih.gov/pubmed/32422375/ doi: 10.1016/j.ijid.2020.05.025 id: cord-283812-ocfjj79v author: Blumberg, Lucille title: Hosting of mass gathering sporting events during the 2013–2016 Ebola virus outbreak in West Africa: experience from three African countries date: 2016-06-15 words: 2834.0 sentences: 125.0 pages: flesch: 46.0 cache: ./cache/cord-283812-ocfjj79v.txt txt: ./txt/cord-283812-ocfjj79v.txt summary: • The 2013–2016 Ebola virus disease (EVD) outbreak in West Africa that resulted in over 28 637 cases and 11 315 deaths required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of EVD. 7, 8 The unprecedented Ebola virus disease (EVD) epidemic in West Africa 9 and the ongoing Zika virus (ZIKV) outbreak in South America 10, 11 were declared Public Health Emergencies of International Concern (PHEIC) by the World Health Organization (WHO) in August 2014 and February 2016, respectively. 4, 14, 15 The 2013-2016 EVD outbreak in West Africa, which resulted in over 28 637 cases and 11 315 deaths, 16 required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of viral haemorrhagic fever (VHF). abstract: • Mass gatherings at sporting events attract millions of international and national host-country travellers, who may put themselves at risk of acquiring local endemic infectious diseases. • The 2013–2016 Ebola virus disease (EVD) outbreak in West Africa that resulted in over 28 637 cases and 11 315 deaths required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of EVD. • Three major sports events were held in Africa during the EVD outbreak, attended by athletes from numerous African countries including Liberia, Sierra Leone, and Guinea, the three countries most affected by EVD: the African Youth Games (Botswana), Africa Cup of Nations (Equatorial Guinea), and All-Africa Games (Republic of Congo). • A large range of infectious diseases other than EVD were considered with respect to the differential diagnosis of acute febrile illnesses and for the provision of laboratory diagnostics and treatment options. • The experience from these three mass gathering events during the Ebola epidemic illustrates that these events can be held safely provided that countries put measures in place for enhanced surveillance and response systems for communicable diseases. url: https://doi.org/10.1016/j.ijid.2016.06.011 doi: 10.1016/j.ijid.2016.06.011 id: cord-349418-98sgr5iv author: Bo, Yacong title: Effectiveness of non-pharmaceutical interventions on COVID-19 transmission in 190 countries from 23 January to 13 April 2020 date: 2020-10-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: To evaluate and compare the effectiveness of four types of non-pharmaceutical interventions (NPIs) in containing the time-varying effective reproduction number (Rt) of COVID-19. METHODS: This study included 1,908,197 confirmed COVID-19 cases from 190 countries between 23 January and 13 April 2020. The implemented NPIs were categorized into four types: mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction (referred to as mandatory mask, quarantine, distancing, and traffic hereafter, respectively). RESULTS: The implementations of mandatory mask, quarantine, distancing and traffic were associated with changes (95%confidence interval, CI) of -15.14% (-21.79% to -7.93%), -11.40% (-13.66% to -9.07%), -42.94% (-44.24% to -41.60%) and -9.26% (-11.46% to -7.01%) in the Rt of COVID-19 compared with those without the implementation of the corresponding measures. Distancing and the simultaneous implementation of two or more types of NPIs seemed to be associated with a greater decrease in the Rt of COVID-19. CONCLUSION: Our study indicates that NPIs can significantly contain the COVID-19 pandemic. Distancing and the simultaneous implementation of two or more NPIs should be the strategic priorities for containing COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33129965/ doi: 10.1016/j.ijid.2020.10.066 id: cord-324295-9c1zxjng author: Bonilla-Aldana, D. Katterine title: Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date: 2020-08-20 words: 3770.0 sentences: 212.0 pages: flesch: 51.0 cache: ./cache/cord-324295-9c1zxjng.txt txt: ./txt/cord-324295-9c1zxjng.txt summary: Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) . abstract: Bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. Transmission of highly pathogenic viruses from bats has been suspected and linked to a spectrum of emerging infectious diseases in humans and animals worldwide. Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we provide a comprehensive review on the diversity, reservoirs, and geographical distribution of the main bat viruses and their potential for cross-species transmission. url: https://www.sciencedirect.com/science/article/pii/S1201971220306809?v=s5 doi: 10.1016/j.ijid.2020.08.050 id: cord-355343-dtdsd8j2 author: Buonsenso, Danilo title: Social consequences of COVID-19 in a low resource setting in Sierra Leone, West Africa date: 2020-06-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Economical and psychological consequences of the lockdown in low-resource setting in rural Africa are unknown. We drafted a survey in order to address the social impact of COVID-19 lockdown on a rural village in Sierra Leone. The survey developed by the study group and translated in the local language, distributed to the householders of the village on April 13(th) and responses collected on April 14(th), when Sierra Leone was on day 11 of lockdown. The questions aimed to assess in the community the following items: age group, main activities before lockdown, change in income and ability to feed the family during lockdown, anxiety during lockdown. 78 householders (100% of Bureh Town) replied. All, expect one, declared a 51-80% (19.2%) to 81-100% (79.4%) reduction of weekly income compared with the pre-lockdown period, declaring difficulties in providing food for the family members (82%), and anxiety (60%). Our analyses showed that people lost their jobs and have difficulties in providing food for their families. url: https://api.elsevier.com/content/article/pii/S1201971220304112 doi: 10.1016/j.ijid.2020.05.104 id: cord-261058-yu2qw02l author: Burgner, David title: Kawasaki disease: What is the epidemiology telling us about the etiology? date: 2005-06-03 words: 5144.0 sentences: 324.0 pages: flesch: 40.0 cache: ./cache/cord-261058-yu2qw02l.txt txt: ./txt/cord-261058-yu2qw02l.txt summary: Thus in genetically susceptible children, acute infections such as those causing fever and rash, may result in unrecognised damage to the cardiovascular system that later manifests itself as adult cardiovascular disease. 3 The consensus view is that KD results from a widely distributed infectious agent (or possibly agents) that causes the clinical syndrome in genetically susceptible children. Kawasaki disease is more common in boys (male:female ratio 1.6:1) 1 a feature observed in many infectious diseases 30, 31 and also in coronary atherosclerosis, where sex differences in immune responses are suggested to mediate susceptibility. A recent report of an association between the presence of genetic material from a novel coronavirus and Kawasaki disease in a handful of cases 48 remains unproven and may reflect an epiphenomenon; the putative etiological agent is a relatively common viral pathogen in young children and it is unclear how long the DNA persists. abstract: Kawasaki disease (KD) is an important and common inflammatory vasculitis of early childhood with a striking predilection for the coronary arteries. It is the predominant cause of paediatric acquired heart disease in developed countries. Despite 40 years of research, the aetiology of KD remains unknown and consequently there is no diagnostic test and treatment is non-specific and sub-optimal. The consensus is that KD is due to one or more widely distributed infectious agent(s), which evoke an abnormal immunological response in genetically susceptible individuals. The epidemiology of KD has been extensively investigated in many populations and provides much of the supporting evidence for the consensus regarding etiology. These epidemiological data are reviewed here, in the context of the etiopathogenesis. It is suggested that these data provide additional clues regarding the cause of KD and may account for some of the continuing controversies in the field. url: https://www.ncbi.nlm.nih.gov/pubmed/15936970/ doi: 10.1016/j.ijid.2005.03.002 id: cord-347499-7q47jh14 author: Burrel, Sonia title: Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19 date: 2020-10-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: We performed a study during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. A second objective consisted in the comparison of the diagnostic performances of URT and LRT samples for SARS-CoV-2 infection and to compare diagnostic performances of upper and lower respiratory tract (URT and LRT) samples for SARS-CoV-2 infection. METHODS: From January 25(th) through March 29(th), 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were tested simultaneously for SARS-CoV-2 and other respiratory viruses. RESULTS: A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age of 50 [1-103] years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% versus 13.4%; P < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. CONCLUSION: The detection of other respiratory viruses in patients during epidemic period cannot rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increases the accuracy of diagnosis of COVID-19. url: https://api.elsevier.com/content/article/pii/S120197122032244X doi: 10.1016/j.ijid.2020.10.040 id: cord-272179-wvw5mmy3 author: Calderaro, Adriana title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 words: 1095.0 sentences: 70.0 pages: flesch: 53.0 cache: ./cache/cord-272179-wvw5mmy3.txt txt: ./txt/cord-272179-wvw5mmy3.txt summary: title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. All novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (Berry et al, 2015) ; SARS-CoV-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children abstract: OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. RESULTS: 474 samples (52.3%) were positive for at least one virus for a total of 583 viruses detected. Single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). RSV (138/583: 23.7%) and RV (130/583: 22.3%) were the most common viruses identified, followed by SARS-CoV2 (82/583: 14.1%). RSV predominates until February with 129 detections and drastically decreases in March to 9 detections. SARS-CoV-2 absent in our area until February 26, in just over a month reached 82 detections. SARS-CoV-2 was found in mixed infections only in 3 cases all observed in children younger than one year old. CONCLUSIONS: This study showed a completely different trend between SARS-CoV-2 and the "common" respiratory viruses that have seen children most affected without distinction of sex, as opposed to SARS-CoV-2 that have seen adult males the most infected. url: https://api.elsevier.com/content/article/pii/S1201971220321895 doi: 10.1016/j.ijid.2020.09.1473 id: cord-277640-vy7ex5lv author: Calderaro, Adriana title: SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby date: 2020-05-14 words: 1171.0 sentences: 63.0 pages: flesch: 52.0 cache: ./cache/cord-277640-vy7ex5lv.txt txt: ./txt/cord-277640-vy7ex5lv.txt summary: The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. To the best of our knowledge, no literature evidence of SARS-CoV-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (Lu and Shi, 2020, Wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. The patient was referred to the Neonatology ward of the University Hospital of Parma (Italy) in the night of Only the culture isolation of this cytopathogenic agent allowed its final identification as SARS-CoV-2. To the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of SARS-CoV-2 infection including virus isolation together with RNA detection were present. abstract: SARS-CoV-2 is emerged in China on December 2019 and now declared pandemic by WHO. We describe the case of an Italian 7-week-old suckling baby SARS-CoV-2-positive only by cell culture method with no clinical suspicion and/or risk factors of SARS-CoV-2 infection. The patient was referred to the hospital with signs and symptoms of infection of the upper respiratory tract before the virus was spread to the province. Nasal and pharyngeal swabs and a nasopharyngeal aspirate were used for conventional and molecular diagnostic assays not including SARS-CoV-2 virus. Bacteria referred to resident population were revealed in nasal and pharyngeal swabs. No viruses were detected using both immunofluorescence assay and nucleic acid amplification assays in the nasopharyngeal aspirate. The baby was discharged in good conditions after 3 days of hospitalization. Later a cytopathic effect on the cell monolayers currently used for respiratory viruses was observed and the viral particles were identified as Coronaviridae by transmission electron microscopy. SARS-CoV-2 was identified by RT-PCR performed both on cell culture and on the stored aliquot of the original sample. The virus isolate was named SARS-Cov-2/human/Parma/1/2020.Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. url: https://api.elsevier.com/content/article/pii/S1201971220303428 doi: 10.1016/j.ijid.2020.05.035 id: cord-293630-zc8huo1j author: Capone, Alessandro title: Simultaneous circulation of COVID-19 and flu in Italy: potential combined effects on the risk of death? date: 2020-08-05 words: 2157.0 sentences: 97.0 pages: flesch: 43.0 cache: ./cache/cord-293630-zc8huo1j.txt txt: ./txt/cord-293630-zc8huo1j.txt summary: Based on data updated to May 20, 2020, in Italy the total recorded number of patients who died due to COVID-19-related reasons is 31,851. While some of the excess mortality reported in the ILI group may be attributable to COVID-19, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? It would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from COVID-19 or influenza. While some of the excess mortality reported in the ILI group (in over 65) may be attributable to COVID-19 infection actually, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? abstract: Based on data updated to May 20, 2020, in Italy the total recorded number of patients who died due to COVID-19-related reasons is 31,851. Demographic and clinical characteristics of died patients (including the number of comorbidities) are extremely relevant, especially to define those with a higher risk of mortality. Health authority recommends flu vaccination in a number of categories at risk of serious medical complications: subjects over 65, patients with diabetes, cardiovascular diseases, COPD, renal failure, cancer, immunodeficiencies, chronic hepatopathies and chronic inflammatory bowel diseases. The peak of the seasonal flu certainly preceded the pandemic one; however, it would seem clear that for a while the two viruses have been circulating simultaneously in Italy. Hence, after its peak, Influenza-like Illness-related (ILI) deaths started to grow again. While some of the excess mortality reported in the ILI group may be attributable to COVID-19, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? A cooperation mechanism intended at establishing an absolute advantage over the host could also be assumed. This system often takes place to boost their reproductive probabilities. A characterization of patients died due to virus-related reasons can be done by cross-linking data stored in different warehouses of the same geographical area and developing electronic health records. It would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from COVID-19 or influenza. The description of the subgroup of patients at higher risk of mortality will be crucial for the prioritization and implementation of future public health prevention and treatment programmes. url: https://doi.org/10.1016/j.ijid.2020.07.077 doi: 10.1016/j.ijid.2020.07.077 id: cord-311413-uiwjrvru author: Chanda-Kapata, Pascalina title: COVID-19 and malaria: A symptom screening challenge for malaria endemic countries date: 2020-04-27 words: 1734.0 sentences: 94.0 pages: flesch: 52.0 cache: ./cache/cord-311413-uiwjrvru.txt txt: ./txt/cord-311413-uiwjrvru.txt summary: COVID-19 currently imposes an additional burden to the already overstretched, resource strapped health services which are grappling to bring under control the high burden of existing infectious and non-infectious diseases, including TB, HIV, and malaria. Health care workers and community members alike are faced with an important challenge of quickly identifying symptoms and taking appropriate steps for laboratory investigation in line with the case definition based on surveillance or clinical characterisation (WHO, 2020a) . Key steps to identifying a COVID-19 case ultimately involves symptomatic or high risk patients presenting to health providers with complaints of any of the following symptoms or travel history: fever, cough, shortness of breath, fatigue, headache and others of acute onset or history of travel to affected areas or contact with an infected person. Thus, current screening approaches for COVID-19 are likely to miss approximately 50% of the infected cases even in countries with good health systems and available diagnostic capacities (Gostic et al., 2020) . abstract: nan url: https://api.elsevier.com/content/article/pii/S120197122030223X doi: 10.1016/j.ijid.2020.04.007 id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 words: 1499.0 sentences: 96.0 pages: flesch: 48.0 cache: ./cache/cord-283590-xvnv17zy.txt txt: ./txt/cord-283590-xvnv17zy.txt summary: Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People''s Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). abstract: The ongoing outbreak of COVID-19 that began in Wuhan, China, has constituted a Public Health Emergency of International Concern, with cases confirmed in multiple countries. Currently, patients are the primary source of infection. We report a confirmed case of COVID-19 whose oropharyngeal swab test of SARS-CoV-2 RNA turned positive in convalescence. This case highlights the importance of active surveillance of SARS-CoV-2 RNA for infectivity assessment. url: https://www.ncbi.nlm.nih.gov/pubmed/32147538/ doi: 10.1016/j.ijid.2020.03.003 id: cord-317624-qdzhncs0 author: Choi, Min Joo title: Comparison of antiviral effect for mild-to-moderate COVID-19 cases between lopinavir/ritonavir versus hydroxychloroquine: A nationwide propensity score-matched cohort study date: 2020-10-27 words: 4287.0 sentences: 228.0 pages: flesch: 49.0 cache: ./cache/cord-317624-qdzhncs0.txt txt: ./txt/cord-317624-qdzhncs0.txt summary: METHODS: Nationwide retrospective case-control study was conducted to compare the effect of HCQ and LPV/r on viral shedding duration among patients with mild-to-moderate COVID-19 using the reimbursement data of National Health Insurance Service. This study aimed to compare the effect of HCQ and LPV/r on the viral shedding duration among patients with mild-to-moderate COVID-19 cases using South Korea''s National Health J o u r n a l P r e -p r o o f Insurance Service (NHIS) database. Among these, only mild-to-moderate grade 1 patients were included in the analysis, and the effect of LPV/r or HCQ use on viral shedding duration was evaluated ( Figure 1 ). In the previous studies including mild COVID-19 patients in CTCs, the mean viral shedding duration from symptom onset was 21-24.5 days, which is longer than the results of our control group , Noh et al., 2020 . abstract: OBJECTIVES: We aimed to compare the antiviral effect of hydroxychloroquine (HCQ) and lopinavir/ritonavir (LPV/r) in patients with COVID-19. METHODS: Nationwide retrospective case-control study was conducted to compare the effect of HCQ and LPV/r on viral shedding duration among patients with mild-to-moderate COVID-19 using the reimbursement data of National Health Insurance Service. After propensity score matching (PSM), multivariate analysis was conducted to determine statistically significant risk factors associated with prolonged viral shedding. RESULTS: Overall, 4,197 patients with mild-to-moderate COVID-19 were included. Patients were categorized into three groups: LPV/r (n = 1,268), HCQ (n = 801), and standard care without HCQ or LPV/r (controls, n = 2128). The median viral shedding duration was 23 (IQR 17–32), 23 (IQR 16–32), and 18 (IQR 12–25) days in the LPV/r, HCQ, and control groups, respectively. Even after PSM, the viral shedding duration was not significantly different between LPV/r and HCQ groups: 23 (IQR, 17–32) days versus 23 (IQR, 16–32) days. On multivariate analysis, old age, malignancy, steroid use, and concomitant pneumonia were statistically significant risk factors for prolonged viral shedding. CONCLUSION: The viral shedding duration was similar between HCQ and LPV/r treatment groups. There was no benefit in improving viral clearance compared to the control group. url: https://www.sciencedirect.com/science/article/pii/S1201971220322669?v=s5 doi: 10.1016/j.ijid.2020.10.062 id: cord-258669-ubw6mdzi author: Colebunders, Robert title: A call for strengthened evidence on targeted, non-pharmaceutical interventions against COVID-19 for the protection of vulnerable individuals in sub-Saharan Africa date: 2020-08-27 words: 2516.0 sentences: 120.0 pages: flesch: 48.0 cache: ./cache/cord-258669-ubw6mdzi.txt txt: ./txt/cord-258669-ubw6mdzi.txt summary: We suggest investigating the feasibility, acceptability, and efficacy of distributing COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. Here, we call for the generation and strengthening of evidence to guide non-pharmaceutical interventions for COVID-19, which we illustrate with a practical proposal for assessing the impact of targeted protection of at-risk individuals in settings in sub-Saharan Africa. Although the early implementation of lockdown measures for COVID-19 control may have contributed to the (initially) low mortality observed in most sub-Saharan Africa countries, the collateral damage resulting from this strategy is becoming increasingly apparent. We therefore propose to complement the extant containment measures in sub-Saharan Africa with more targeted protection strategies, aiming at protecting people at risk of severe COVID-19 disease. One strategy could be to distribute COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. abstract: Since many sub-Saharan African countries started easing their lockdown measures, COVID-19 cases have been on the rise. As COVID- 19 transmission may be difficult to stop in these settings, we propose to complement the existing COVID-19 prevention strategies aiming at reducing overall transmission with more targeted strategies to protect people at risk for severe COVID-19 disease. We suggest investigating the feasibility, acceptability, and efficacy of distributing COVID-19 prevention kits to households with persons at increased risk for severe COVID-19 disease. url: https://www.sciencedirect.com/science/article/pii/S1201971220306871?v=s5 doi: 10.1016/j.ijid.2020.08.060 id: cord-268883-nf4fm7r7 author: Corchuelo, Jairo title: Oral manifestations in a patient with a history of asymptomatic COVID-19. Case Report date: 2020-09-01 words: 1679.0 sentences: 92.0 pages: flesch: 49.0 cache: ./cache/cord-268883-nf4fm7r7.txt txt: ./txt/cord-268883-nf4fm7r7.txt summary: This case shows that the problems that arise in the oral mucosa in patients with suspected or confirmed SARS-CoV-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technology currently available worldwide. Due to the use of intensified therapeutic methods possibly aggravated by SARS-CoV-2, an increase in cases with oropharyngeal symptoms / conditions, dental-oral problems associated with soft tissues, saliva production (dry mouth) as side effects, could be predicted, even after recovering from COVID-19. Taking into account that Candida albicans is part of the oral microbiome and that there were favorable events for its pathological development, such as the decrease in salivation manifested in the patient by the sensation of dry mouth, in addition to the frequent use of antibiotics and a mild predisposing factor such as the female sex (Zegarelli 1993) and the successful response to nystatin treatment, we can clinically confirm candida infection The hyperpigmentation of the gums in the anterior teeth due to the aesthetic problem that it represents for the patient is the one that causes of most concern. abstract: The pandemic situation has led to public health measures that have forced patients with and without the SARS-CoV-2 virus to remain isolated and take steps to prevent the spread. Many of these patients have been unable to attend the control of medical-dental services, which in many cases complicates their situation. This study reports on the oral manifestations of an asymptomatic COVID-19 patient treated interdisciplinary by teleconsultation due to the sudden appearance of lesions in the oral mucosa. Lesions are diagnosed, therapeutic measures are taken, and improvement is shown. This case shows that the problems that arise in the oral mucosa in patients with suspected or confirmed SARS-CoV-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technology currently available worldwide. It also decreases the risk of transmission of SARS-Cov-2 between patients and health professionals. url: https://api.elsevier.com/content/article/pii/S1201971220307001 doi: 10.1016/j.ijid.2020.08.071 id: cord-272015-1anph6qi author: Dauby, Nicolas title: The unfinished story of hydroxychloroquine in COVID-19: the right anti-inflammatory dose at the right moment? date: 2020-10-17 words: 959.0 sentences: 65.0 pages: flesch: 43.0 cache: ./cache/cord-272015-1anph6qi.txt txt: ./txt/cord-272015-1anph6qi.txt summary: The observation by Lammers et al (Lammers et al.) that early HCQ treatment after admission at low dosage (2400 mg in total) is associated with lower risk of admission in intensive care unit coincides with large observational studies showing a lower mortality rate in patients exposed to HCQ therapy compared to no or other treatment. Another recent large cohort study of patients on low-dose HCQ for inflammatory disorders reported an association between chronic HCQ use and reduced mortality following SARS-CoV-2 infection (Gentry et al. The association of treatment with hydroxychloroquine and hospital mortality in COVID-19 patients Low-dose hydroxychloroquine therapy and mortality in hospitalised patients with COVID-19: a nationwide observational study of 8075 participants Use of hydroxychloroquine in hospitalised COVID-19 patients is associated with reduced mortality: Findings from the observational multicentre Italian CORIST study Longterm hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220322360?v=s5 doi: 10.1016/j.ijid.2020.10.032 id: cord-338225-8dlxnpcn author: De Meyer, Sandra title: Lack of Antiviral Activity of Darunavir against SARS-CoV-2 date: 2020-05-29 words: 329.0 sentences: 27.0 pages: flesch: 60.0 cache: ./cache/cord-338225-8dlxnpcn.txt txt: ./txt/cord-338225-8dlxnpcn.txt summary: Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. Overall, the data do not support use of darunavir for treatment of COVID-19 CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as 23 therapeutic alternatives. abstract: Abstract Objectives Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Methods Prezcobix/Rezolsta is a fixed-dose combination of 800mg of the HIV protease inhibitor darunavir (DRV) and 150mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. There are currently no definitive data on the safety and efficacy of DRV/cobicistat for treatment of COVID-19. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. Results DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100μM). Remdesivir, used as a positive control, showed potent antiviral activity (EC50 =0.38μM). Conclusions Overall, the data do not support the use of DRV for treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32479865/ doi: 10.1016/j.ijid.2020.05.085 id: cord-274028-dvsvtsn0 author: Del Brutto, Oscar H. title: SARS-CoV-2-related mortality in a rural Latin American population date: 2020-08-08 words: 1217.0 sentences: 74.0 pages: flesch: 60.0 cache: ./cache/cord-274028-dvsvtsn0.txt txt: ./txt/cord-274028-dvsvtsn0.txt summary: Here, we report SARS-CoV-2 mortality rates in Atahualpa residents aged ≥18 years. Twenty-J o u r n a l P r e -p r o o f seven out of the 29 deaths likely related to SARS-CoV-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). The overall mortality rate in Atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% C.I.: 15.9 -29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 -22.4 ). When SARS-CoV-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47. In Atahualpa, SARS-CoV-2 rapidly spread across the village, markedly increasing mortality during April and May, 2020 (Figure 1) , and infecting 45% of the adult population, in just a few months [6] . abstract: A sudden increase in adult mortality associated with respiratory diseases was noticed in Atahualpa (a rural Ecuadorian village), coinciding with the introduction of SARS-CoV-2 in the region. From a total of 1,852 individuals aged ≥18 years, 40 deaths occurred between January and June, 2020. In addition, a seroprevalence survey showed that 45% of the adult population have SARS-CoV-2 antibodies. Verbal autopsies revealed SARS-CoV-2 as the most likely cause of death in 29 cases. The mean age of suspected or confirmed SARS-CoV-2 cases was 76.9 ± 12.1 years, while that of those dying from unrelated causes was 60.3 ± 20.4 years (p = 0.003). The overall mortality rate was 21.6 per 1,000 population (95% C.I.: 15.9 – 29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 – 22.4). This configures a 266% of excess mortality when compared to 5.9 per 1,000 (95% C.I.: 3.3 – 10.6) deaths from other causes. When SARS-CoV-2 mortality rate was calculated in individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47.8 – 98.4). After peaking in April and May, mortality significantly decreased. It is possible that the high proportion of infected individuals and the resulting herd immunity contributed to the observed reduction in mortality. url: https://www.ncbi.nlm.nih.gov/pubmed/32781165/ doi: 10.1016/j.ijid.2020.08.003 id: cord-328459-nmd81sue author: Dioscoridi, Lorenzo title: Covid-19 exposure risk for family members of healthcare workers: an observational study date: 2020-07-04 words: 1243.0 sentences: 78.0 pages: flesch: 60.0 cache: ./cache/cord-328459-nmd81sue.txt txt: ./txt/cord-328459-nmd81sue.txt summary: However, no available papers discussed the risk of exposure of family members (FM) of HWs. Aims The present study collected the data of SARS-COV-2 positive FM of HWs using serological rapid IgM/IgG tests (SRT) compared with positive HWs at SRT and serological quantitative IgG test (SQT). The key element of our study was to assess the total number of family members (FM) of HWs positive to SARS-COV-2 infection and the number of positive HWs working in a COVID-19 hospital. The SRT studied both IgG and IgM with a declared sensitivity of 100% for IgG and 85% for IgM SQT used in the study was ELISA test researching IgG anti-S1/anti-S2 for SARS-CoV-2, available and validated for HWs screening in the region of the study (Lombardia, Italy). For both HWs and FMs, exposure to COVID-19 cases, onset of suspicious symptoms (also before the study period since the 1 st February 2020), photos of the serological tests after 10 minutes, serological tests'' platforms, past medical history, drugs and clinical course were registered. abstract: Abstract Background Many papers considered the exposure risk to COVID-19 of general population and healthcare workers (HW). However, no available papers discussed the risk of exposure of family members (FM) of HWs. Aims The present study collected the data of SARS-COV-2 positive FM of HWs using serological rapid IgM/IgG tests (SRT) compared with positive HWs at SRT and serological quantitative IgG test (SQT). Methods The study was conducted from 2nd to 31th May 2020. 38 HWs were tested by both SRT and SQT; 81 FMs were screened using SRT. Descriptive statistical analyses were used to summarize the data. Results Of the 38 HWs, 2 (5,3%) showed IgG line at SRT, confirmed by SQT. 32 HWs decided self-isolation from the family during SARS-COV-2 spreading. Out of 81 FMs, 26 (32,1%) were found IgG positive at SRT. 11 (42%) of them had symptoms typical for COVID-19 in the study period. In two families, the HWs were the only negative case. Conclusions General population’s exposure to COVID-19 was less controlled than HWs’ one. HWs experienced lower infection’s rate than their families and did not represented a risk of transmission for relatives. url: https://www.ncbi.nlm.nih.gov/pubmed/32634587/ doi: 10.1016/j.ijid.2020.06.106 id: cord-262310-z0m6uuzf author: Effenberger, Maria title: Association of the COVID-19 pandemic with Internet Search Volumes: A Google TrendsTM Analysis date: 2020-04-17 words: 2774.0 sentences: 145.0 pages: flesch: 59.0 cache: ./cache/cord-262310-z0m6uuzf.txt txt: ./txt/cord-262310-z0m6uuzf.txt summary: Methods We performed a Google TrendsTM search for "Coronavirus" and compared Relative Search Volumes (RSV) indices to the number of reported COVID-19 cases by the European Center for Disease Control (ECDC) using time-lag correlation analysis. The worldwide Google TrendsTM index reached its peak on the 12th of March 2020 at a time when numbers of infected patients started to increase in Europe and COVID-19 was declared a pandemic. In European countries, especially in Italy, a small peak in the Google Trends TM analysis was found during the outbreak in China and a climax was found on February 23 rd 2020, a few days before the numbers of newly COVID-19 started to increase exponentially. The peak of search queries was March 3 rd a new increase in RSV is found in Brazil, followed by increasing numbers of newly confirmed cases of COVID-19 ( Figure 2 ). abstract: Abstract Objectives To assess the association of public interest in coronavirus infections with the actual number of infected cases for selected countries across the globe. Methods We performed a Google TrendsTM search for “Coronavirus” and compared Relative Search Volumes (RSV) indices to the number of reported COVID-19 cases by the European Center for Disease Control (ECDC) using time-lag correlation analysis. Results Worldwide public interest in Coronavirus reached its first peak end of January when numbers of newly infected patients started to increase exponentially in China. The worldwide Google TrendsTM index reached its peak on the 12th of March 2020 at a time when numbers of infected patients started to increase in Europe and COVID-19 was declared a pandemic. At this time the general interest in China but also the Republic of Korea has already been significantly decreased as compared to end of January. Correlations between RSV indices and number of new COVID-19 cases were observed across all investigated countries with highest correlations observed with a time lag of -11.5 days, i.e. highest interest in coronavirus observed 11.5 days before the peak of newly infected cases. This pattern was very consistent across European countries but also holds true for the US. In Brazil and Australia, highest correlations were observed with a time lag of -7 days. In Egypt the highest correlation is given with a time lag of 0, potentially indicating that in this country, numbers of newly infected patients will increase exponentially within the course of April. Conclusions Public interest indicated by RSV indices can help to monitor the progression of an outbreak such as the current COVID-19 pandemic. Public interest is on average highest 11.5 days before the peak of newly infected cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32305520/ doi: 10.1016/j.ijid.2020.04.033 id: cord-293247-ltxt2dfv author: Elachola, Habida title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings date: 2015-10-09 words: 1233.0 sentences: 57.0 pages: flesch: 44.0 cache: ./cache/cord-293247-ltxt2dfv.txt txt: ./txt/cord-293247-ltxt2dfv.txt summary: title: Advancing the global health security agenda in light of the 2015 annual Hajj pilgrimage and other mass gatherings Although current GHSA is yet to specifically highlight mass gathering preparedness as a strategic priority even in countries with high participant contribution to mass gatherings, the 12 Global Health Security Agenda action packages and the strategies to minimize the implications of mass gathering on public health are similar. Given that two-thirds of the emerging diseases are zoonotic, human-animal interaction during some mass gatherings such as the Hajj further increases the risk, and Saudi Arabia imports sacrifice animals from 6 countries. Mass gatherings offer opportunities to implement, test, and assess GHSA objectives in its entirety and can contribute significantly to health security of individuals, nations, and the world. Mass gatherings medicine and global health security abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971215002374 doi: 10.1016/j.ijid.2015.10.003 id: cord-268037-szhzmzys author: Eshaghi, A. title: A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains date: 2008-12-17 words: 806.0 sentences: 54.0 pages: flesch: 46.0 cache: ./cache/cord-268037-szhzmzys.txt txt: ./txt/cord-268037-szhzmzys.txt summary: authors: Eshaghi, A.; Blair, J.; Burton, L.; Lombos, E.; Choi, K.; De Lima, C.; Drews, S.J. title: A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains A paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with H274Y-positive influenza A (H1N1) strains The purpose of this brief investigation was to determine whether nasopharyngeal specimens from patients infected with strains of influenza A (H1N1) carrying the H274Y mutation were more likely than not to contain other commonly circulating respiratory viral pathogens. Isolate sequences were compared to sequences with described H274Y mutations: GenBank accession No. 7 Specimens corresponding to H274Y mutant and H274 wild-type isolates were blinded and chosen at random for a retrospective investigation for other respiratory viral pathogens (adenovirus, coronavirus 229E/NL63, coronavirus OC43, influenza A/B, parainfluenza virus 1/2/3, respiratory syncytial virus A/B, rhinovirus A) using the Seeplex 1 RV detection kit protocol (Seegene, Inc., Rockville, MD). abstract: nan url: https://doi.org/10.1016/j.ijid.2008.07.026 doi: 10.1016/j.ijid.2008.07.026 id: cord-340279-bq5owwot author: Espíndola, Otávio de Melo title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid date: 2020-06-04 words: 285.0 sentences: 37.0 pages: flesch: 52.0 cache: ./cache/cord-340279-bq5owwot.txt txt: ./txt/cord-340279-bq5owwot.txt summary: key: cord-340279-bq5owwot title: Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid cord_uid: bq5owwot Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. • SARS-CoV-2 RNA is mainly undetectable in the cerebrospinal fluid. • SARS-CoV-2 clearance in the cerebrospinal fluid may precede the neurological involvement. • Common neuropathogens should be investigated in the CSF of COVID-19 patients. CSF analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (Table 2) . Status of SARS-CoV-2 in 127 cerebrospinal fluid of patients with COVID-19 and stroke Guillain-Barré syndrome related 130 to COVID-19 infection Two patients with 132 acute meningo-encephalitis concomitant to SARS-CoV-2 infection Guillain-Barré syndrome as 137 a complication of SARS-CoV-2 infection Neurologic Features in Severe 141 SARS-CoV-2 Infection abstract: Abstract We report that patients with COVID-19 displaying distinct neurological disorders have undetectable or extremely low levels of SARS-CoV-2 RNA in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. This finding points to the need for the development of more sensitive molecular tests and the investigation of other neurotropic pathogens to exclude concurrent neuroinfection. url: https://doi.org/10.1016/j.ijid.2020.05.123 doi: 10.1016/j.ijid.2020.05.123 id: cord-330136-o8df8szx author: Fan, Hua title: Cardiac injuries in patients with coronavirus disease 2019: Not to be ignored date: 2020-05-11 words: 2167.0 sentences: 133.0 pages: flesch: 54.0 cache: ./cache/cord-330136-o8df8szx.txt txt: ./txt/cord-330136-o8df8szx.txt summary: 40 non-survivors had test result of hs-TnI，they were divided into two groups based on cardiac injury，Further analysis revealed that non-survivors with elevated hs-TnI levels on admission had shorter duration from symptom onset to death, and TnI elevation was related to the dismal prognosis. The mortality of critically ill COVID-19 patients is high, but its mechanism is not clear at present, and it might be related to the virus-induced acute lung injury, inflammatory factor storm. Our study discovered that the level of hs-TnI increased in many patients on admission, indicating that cardiac injury occurred in the early stage of the disease.The incidence rate of cardiac injury among patients at admission was 16.44%, with the non-survivors having an incidence rate of as high as 25.53%. Association of Cardiac Injury With Mortality in Hospitalized Patients With COVID-19 in Wuhan, China abstract: Abstract Objective To describe the clinical features of coronavirus disease 2019 (COVID-19). Methods We recruited 73 patients with COVID-19 [49 men and 24 women; average age: 58.36 years (SD: 14.31)] admitted to the intensive care unit of Wuhan Jinyintan Hospital from December 30, 2019 to February 16, 2020. Demographics, underlying diseases, and laboratory test results on admission were collected and analyzed. Data were compared between survivors and non-survivors. Results The non-survivors were older (65.46 [SD 9.74] vs 46.23 [12.01]) and were more likely to have chronic medical illnesses. Non-survivors tend to develop more severe lymphopenia, with higher C-reactive protein, interleukin-6, D-dimer, and hs-Troponin I(hs-TnI) levels. Patients with elevated hs-TnI levels on admission had shorter duration from symptom onset to death. Increased hs-TnI level was related to dismal prognosis. Death risk increased by 20.8% when the hs-TnI level increased by one unit. After adjusting for inflammatory or coagulation index, the independent predictive relationship between hs-TnI and death disappeared. Conclusions Cardiac injury may occur at the early stage of COVID-19, which is associated with high mortality. Inflammatory factor cascade and coagulation abnormality may be the potential mechanisms of COVID-19 combined with cardiac injury. url: https://doi.org/10.1016/j.ijid.2020.05.024 doi: 10.1016/j.ijid.2020.05.024 id: cord-320902-1hfxju5f author: Filocamo, Giovanni title: Use of anakinra in severe COVID-19: a case report date: 2020-05-11 words: 1440.0 sentences: 88.0 pages: flesch: 46.0 cache: ./cache/cord-320902-1hfxju5f.txt txt: ./txt/cord-320902-1hfxju5f.txt summary: As of March 25 2020, in Lombardy, Italy, 1591 patients were admitted in ICUs, of them, 405 (26%) had died in ICU, 256 (16%) had been discharged from the ICU, while 920 patients (58%) were still in the ICU The IL-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as Still''s disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). At day 10, considering the patient''s critical conditions (PaO2/FiO2 85, volume control ventilation PEEP 14 FiO2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. Indeed, IL-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with sHLH associated to viral infections such as EBV, H1N1 and Ebola (10). abstract: Abstract Coronavirus Disease 19 is a global healthcare emergency with high lethality rate. Relevant inflammatory cytokine storm is associated with severity of disease and IL1 inhibition is a cornerstone treatment for hyperinflammatory diseases. We present here the case of a patient with critical COVID-19 successfully treated with IL-1 receptor antagonist (anakinra). url: https://api.elsevier.com/content/article/pii/S1201971220303337 doi: 10.1016/j.ijid.2020.05.026 id: cord-340410-s9haq8y1 author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-06-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Rapid detection of SARS-CoV-2 is critical for the diagnosis of coronavirus disease 2019 (COVID-19) and preventing the spread of the virus. A novel “2019 Novel Coronavirus Detection Kit (nCoV-DK)” halves detection time by eliminating the steps of RNA extraction and purification. We evaluated concordance between the nCoV-DK and direct PCR. The virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct PCR and nCoV-DK, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. The nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. url: https://doi.org/10.1016/j.ijid.2020.06.074 doi: 10.1016/j.ijid.2020.06.074 id: cord-292092-o6s5nw49 author: Furuse, Yuki title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 date: 2015-09-30 words: 1232.0 sentences: 77.0 pages: flesch: 60.0 cache: ./cache/cord-292092-o6s5nw49.txt txt: ./txt/cord-292092-o6s5nw49.txt summary: title: Conservation of nucleotide sequences for molecular diagnosis of Middle East respiratory syndrome coronavirus, 2015 The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. 5 The laboratory diagnosis of MERS-CoV infection is mainly performed using real-time reverse transcription PCR (RT-PCR) to detect viral RNA in specimens. This study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the RT-PCR protocols for the molecular diagnosis of MERS-CoV infections. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Table 1 Conservation of the primer and probe region sequences of the WHO-recommended assays for the molecular diagnosis of MERS-CoV abstract: Infection due to the Middle East respiratory syndrome coronavirus (MERS-CoV) is widespread. The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. Although the diagnostic protocols were established only 2 years ago, mismatches between the sequences of primers/probes and viruses were found for several of the assays. Such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. A slight modification in the primer design is suggested. Protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as MERS-CoV. url: https://api.elsevier.com/content/article/pii/S1201971215002283 doi: 10.1016/j.ijid.2015.09.018 id: cord-339576-0d6sa9pe author: Guallar, María Pilar title: Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity date: 2020-06-14 words: 1380.0 sentences: 79.0 pages: flesch: 56.0 cache: ./cache/cord-339576-0d6sa9pe.txt txt: ./txt/cord-339576-0d6sa9pe.txt summary: Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. Herein we report three clusters of SARS-CoV-2 infection in Madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. In this cluster, low viral exposures along with social distancing would J o u r n a l P r e -p r o o f account for more benign clinical forms of COVID-19, along with asymptomatic and uninfected cases. In this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of COVID-19, being all residents infected. In this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. Timeframe of SARS-CoV-2 infections and COVID-19 disease severity in persons belonging to groups with different viral exposure abstract: Abstract A relationship between the infecting dose and the risk of disease severity has not been demonstrated for SARS-CoV-2 infection. Here, we report three clusters of individuals that were exposed to diverse inoculi in Madrid and overall developed divrgent clinical forms of COVID-19. Our data support that a greater SARS-CoV-2 inoculi at the time of exposure might determine a higher risk of severe COVID-19. url: https://api.elsevier.com/content/article/pii/S1201971220304707 doi: 10.1016/j.ijid.2020.06.035 id: cord-311479-8pjoz64q author: He, Daihai title: The relative transmissibility of asymptomatic cases among close contacts date: 2020-04-18 words: 815.0 sentences: 58.0 pages: flesch: 57.0 cache: ./cache/cord-311479-8pjoz64q.txt txt: ./txt/cord-311479-8pjoz64q.txt summary: A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. A recent 24 study in China showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. 28 29 Keywords: COVID-19; asymptomatic cases; relative transmissibility 30 31 32 33 Main text 35 Nishiura et al (Nishiura et al, 2020 ) estimated the asymptomatic ratio of COVID-19 was 41.6% 36 (5 out of 12 confirmed cases) among 565 Japanese individuals evacuated from Wuhan, China. The odds ratio (OR) is estimated 109 In summary, we conclude that the relatively transmissibility of asymptomatic case could be 127 significantly smaller than that of the symptomatic cases. Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-158 19) Estimating the asymptomatic 161 proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess 162 cruise ship abstract: Abstract Asymptomatic transmission of the coronavirus disease 2019 is an important topic. A recent study in China showed that transmissibility of the asymptomatic cases is comparable to that of symptomatic cases. Here we showed that the conclusion may depend on how we interpret the data. To the best of our knowledge, this is the first time the relative transmissibility of asymptomatic COVID-19 cases is quantified. url: https://www.sciencedirect.com/science/article/pii/S1201971220302502?v=s5 doi: 10.1016/j.ijid.2020.04.034 id: cord-330692-rqwkkfp0 author: He, Daihai title: Comparing COVID-19 and the 1918–19 influenza pandemics in United Kingdom date: 2020-06-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract We compare the COVID-19 pandemic and 1918-19 influenza pandemic in United Kingdom. We found that the on-going COVID-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. We discussed the similar characteristics between these two pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32599281/ doi: 10.1016/j.ijid.2020.06.075 id: cord-273090-fdzkfo1u author: He, Susu title: Relationship between Chest CT manifestations and immune response in COVID-19 patients date: 2020-06-20 words: 2816.0 sentences: 140.0 pages: flesch: 58.0 cache: ./cache/cord-273090-fdzkfo1u.txt txt: ./txt/cord-273090-fdzkfo1u.txt summary: In critically ill patients, the decrease of absolute value of CD4 + T cells and increase of IL-6 level are significantly correlated with the volume of lung lesions. There have been many reports that most of the 2019-nCoV patients have chest CT manifestations of pneumonia, typically showing bilateral ground-glass shadows and patchy shadows, and a few can also appear as consolidation shadows and interstitial lesions, the laboratory showed that the lymphocytes count in most patients decreased [6] [7] [8] [9] , with gradually worsened the disease, the lymphocytes absolute count continued to decline [9] , and has been There are reports in the literature that the proinflammatory cytokines IL-2, IL-6, IL-8, IL-10, and TNF-α are elevated in some 2019-nCoV patients [7] [8] . The purpose of this study is to investigate changes in lymphocytes counts and cytokines levels induced by 2019-nCoV and their effects on lung lesions, to determine the severity of the disease, and to select markers that could prompt early clinical intervention. abstract: Abstract Objectives To study the and correlations of lymphocytes and cytokines between changes of lung lesion volumes in patients with COVID-19, and to predict their correlation. Methods 93 patients with COVID-19 were divided into mild and severe groups. The data of lymphocyte subgroups and cytokines were collected, the imaging characteristics were measured and correlation analysis was performed to analyze the differences. Results 60 mild and 33 severe patients were included, Lymphocyte subsets decreased in both groups. The percentages of reduction of absolute lymphocytes value in mild and severe groups were 32% and 64% respectively. The lung CT lesion volume of all patients was 241.45 ± 282.92 cm3, among which the mild group was 151.29 ± 226.04 cm3 and the severe group was 405.38 ± 304.90 cm3, respectively. In critically ill patients, the decrease of absolute value of CD4 + T cells and increase of IL-6 level are significantly correlated with the volume of lung lesions. Conclusions The absolute values of CD3+, CD4+, and CD8 + T cells are lower in patients with COVID-19, the levels of IL-6 and IL-10 are increased. The severity of lung lesions predicts poor clinical outcomes and may be a predictor of the transition from mild to severe. url: https://doi.org/10.1016/j.ijid.2020.06.059 doi: 10.1016/j.ijid.2020.06.059 id: cord-320829-uepneyug author: He, Zhongping title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 words: 2631.0 sentences: 138.0 pages: flesch: 59.0 cache: ./cache/cord-320829-uepneyug.txt txt: ./txt/cord-320829-uepneyug.txt summary: title: Effects of severe acute respiratory syndrome (SARS) coronavirus infection on peripheral blood lymphocytes and their subsets DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Effects of severe acute respiratory syndrome (SARS) coronavirus infection 327 Figure 3 Kinetics of lymphocyte subsets (expressed as mean number of cells  10 6 /L) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed SARS patients, and in otherwise healthy controls. A study of 75 patients from the Amoy Gardens outbreak in Hong Kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ARDS), oxygen saturation and gastrointestinal symptoms in these two cohorts. Kinetics of severe acute respiratory syndrome (SARS) coronavirus-specific antibodies in 271 laboratory-confirmed cases of SARS abstract: INTRODUCTION: Severe acute respiratory syndrome (SARS) caused large outbreaks of atypical pneumonia in 2003, with the largest localized outbreak occurring in Beijing, China. Lymphopenia was prominent amongst the laboratory abnormalities reported in acute SARS. METHODS: The effect of SARS on peripheral blood lymphocytes and their subsets was examined in 271 SARS coronavirus-infected individuals. RESULTS: There was a significant decrease in the CD45+, CD3+, CD4+, CD8+, CD19+ and CD16+/56+ cell counts over the five weeks of the SARS illness although CD4+/CD8+ ratios did not change significantly. The lymphopenia was prolonged, reaching a nadir during days 7–9 in the second week of illness before returning towards normal after five weeks, with the lowest mean CD4+ cell count of 317 cells × 10(6)/L at day 7, and CD8+ cell count of 239 cells × 10(6)/L at day 8. Patients with more severe clinical illness, or patients who died, had significantly more profound CD4+ and CD8+ lymphopenia. DISCUSSION: Lymphopenia is a prominent part of SARS-CoV infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. Possible reasons for the SARS-associated lymphopenia may be direct infection of lymphocytes by SARS-CoV, lymphocyte sequestration in the lung or cytokine-mediated lymphocyte trafficking. There may also be immune-mediated lymphocyte destruction, bone marrow or thymus suppression, or apoptosis. url: https://api.elsevier.com/content/article/pii/S120197120500072X doi: 10.1016/j.ijid.2004.07.014 id: cord-300774-5mrkmctl author: Hernández-Mora, Miguel Górgolas title: Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia date: 2020-10-25 words: 4340.0 sentences: 230.0 pages: flesch: 50.0 cache: ./cache/cord-300774-5mrkmctl.txt txt: ./txt/cord-300774-5mrkmctl.txt summary: INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). Patients with severe SARS-CoV-2 pneumonia (SSP) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . However, clinical and pathological studies of SARS-CoV-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . abstract: INTRODUCTION: Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). However, there are no consistent data whom might benefit most from it. METHODS: We provided tocilizumab on a compassionate-use basis to patients with SSP hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. Primary endpoint was intubation or death after 24 hours of its administration. Patients received at least one dose of 400 mg intravenous tocilizumab during March 8-2020, through April 20-2020. RESULTS: A total of 207 patients were studied and 186 analysed. The mean age was 65 years and 68% were male. A co-existing condition was present in 68 % of cases. Death prognostic factors were older age, higher IL-6, D-dimer and high sensitivity C reactive protein (HSCRP), lower total lymphocytes and severe disease requiring higher oxygen support. The primary endpoint (intubation or death) was significantly worst (37% vs 13%, p < 0·001) in those receiving the drug when the oxygen support was high (FiO2 > 0.5%). CONCLUSIONS: Tocilizumab is well tolerated in patients with severe SARS-CoV-2 pneumonia, but it has a limited effect on the evolution of cases with high oxygen support needs. url: https://www.sciencedirect.com/science/article/pii/S1201971220322499?v=s5 doi: 10.1016/j.ijid.2020.10.045 id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 words: 3105.0 sentences: 184.0 pages: flesch: 55.0 cache: ./cache/cord-258250-zueo1xfa.txt txt: ./txt/cord-258250-zueo1xfa.txt summary: title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . abstract: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is determined by reverse-transcription PCR (RT-PCR) in routine clinical practice. In the current pandemic situation, a more rapid and high-throughput method is in growing demand. Here, we validated the performance of a new antigen test (LUMIPULSE) based on the chemiluminescence enzyme immunoassay. A total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients, 231 individual samples from 4 infected patients and 215 non-infected individuals) were analyzed for SARS-CoV-2 by quantitative RT-PCR (RT-qPCR) and then subjected to LUMIPULSE. We determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of RT-qPCR. Further, we compared the viral loads and antigen levels in serial samples from seven infected patients. When using RT-qPCR as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313). In specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with RT-qPCR, respectively. This concordance declined with lower viral loads. In the serially followed patients, the antigen levels showed a steady decline along with viral clearance. This gradual decline was in contrast with the abrupt “positive-to-negative” and “negative-to-positive” status changes observed with RT-qPCR, particularly in the late phase of infection. In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. url: https://doi.org/10.1016/j.ijid.2020.08.029 doi: 10.1016/j.ijid.2020.08.029 id: cord-265146-j0n3a4m6 author: Hsieh, Ying-Hen title: Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan date: 2013-02-12 words: 4147.0 sentences: 192.0 pages: flesch: 58.0 cache: ./cache/cord-265146-j0n3a4m6.txt txt: ./txt/cord-265146-j0n3a4m6.txt summary: Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. RESULTS: Model fit revealed a two-wave epidemic during April 2004–March 2007. Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. Results: Model fit revealed a two-wave epidemic during April 2004-March 2007. Correlation analysis was performed in an attempt to determine the relationship between the male and female IDUs. The data used here were extracted from the monthly reported HIV case data between April 2004 and March 2007, for a total of 36 months, made available by the Taiwan Centers for Disease Control and Prevention (TCDC) on the TCDC website. The monthly time series data of reported HIV cases for male IDUs, female IDUs, and all IDUs in Taiwan were fit to the Richards model as in Figure 1 and Table 1 The effective reproduction number R was computed for each wave. abstract: OBJECTIVE: To ascertain the explosive 2004–2006 outbreak of HIV-1 CRF07_BC among intravenous drug users (IDU) in Taiwan, which more than doubled the total number of reported HIV cases in less than 3 years, resulting in a 45-fold increase in cumulative IDU/HIV cases and a 40-fold increase in previously seldom-reported female IDU/HIV cases. METHODS: A mathematical model was utilized to fit the monthly case data, in order to estimate the turning points (peak incidence) and the reproduction number R of the outbreak. Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. RESULTS: Model fit revealed a two-wave epidemic during April 2004–March 2007. The larger second wave started shortly after May 2005 and peaked in October 2005 before gradually subsiding. R was estimated to be 3.15 (3.14–3.16) and 27.21 (26.73–28.05) for the two respective waves. The time series of monthly differences in male and female case data were found to be most significantly correlated at lag 0 (i.e., r > 0.7) with r = 0.906 and 0.804, respectively in each direction. The Granger causality test indicated that the male time series caused the corresponding female time series with a lag of 2 months or less. CONCLUSIONS: The modeling results revealed the presence of a small first wave in 2004, before an explosion of cases after May 2005. Furthermore, a harm reduction program implemented in August 2005 contributed to the downturn in the epidemic after October. Correlation results also suggest that the upsurge in male HIV cases led to the subsequent drastic surge in female cases. url: https://doi.org/10.1016/j.ijid.2013.01.002 doi: 10.1016/j.ijid.2013.01.002 id: cord-283891-m36un1y2 author: Hu, Bisong title: First, second and potential third generation spreads of the COVID-19 epidemic in mainland China: an early exploratory study incorporating location-based service data of mobile devices date: 2020-05-17 words: 4656.0 sentences: 220.0 pages: flesch: 47.0 cache: ./cache/cord-283891-m36un1y2.txt txt: ./txt/cord-283891-m36un1y2.txt summary: Methods We used spatiotemporal data of COVID-19 cases in mainland China and two categories of location-based service (LBS) data of mobile devices from the primary and secondary epidemic sources to calculate Pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. Here, using location-based service (LBS) data of mobile devices, we analyzed the spatiotemporal association of the confirmed COVID-19 cases and human movements from the sources of the epidemic outbreak, and revealed the first, second and potential third generation spreads of the COVID-19 epidemic in mainland China. Based on the above datasets of COVID-19 cases in mainland China and two categories of location-based service data of mobile devices from the epidemic sources, we calculated their Pearson correlation coefficient, r, and spatial stratified heterogeneity (SSH), q, statistics. abstract: Abstract Objectives The outbreak of atypical pneumonia caused by the novel coronavirus (COVID-19) has currently become a global concern. The generations of the epidemic spread are not well known, yet these are critical parameters to facilitate an understanding of the epidemic. A seafood wholesale market and Wuhan city, China, were recognized as the primary and secondary epidemic sources. Human movements nationwide from the two epidemic sources revealed the characteristics of the first-generation and second-generation spreads of the COVID-19 epidemic, as well as the potential third-generation spread. Methods We used spatiotemporal data of COVID-19 cases in mainland China and two categories of location-based service (LBS) data of mobile devices from the primary and secondary epidemic sources to calculate Pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. Results Two categories of device trajectories had generally significant correlations and determinant powers of the epidemic spread. Bothr and q statistics decreased with distance from the epidemic sources and their associations changed with time. At the beginning of the epidemic, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. They strongly interacted to enhance the epidemic in Hubei province and the trend was also significant in the provinces adjacent to Hubei. The third-generation spread started in Wuhan from January 17 to 20, 2020, and in Hubei from January 23 to 24. No obvious third-generation spread was detected outside Hubei. Conclusions The findings provide important foundations to quantify the effect of human movement on epidemic spread and inform ongoing control strategies. The spatiotemporal association between the epidemic spread and human movements from the primary and secondary epidemic sources indicates a transfer from second to third generations of the infection. Urgent control measures include preventing the potential third-generation spread in mainland China, eliminating it in Hubei, and reducing the interaction influence of first-generation and second-generation spreads. url: https://doi.org/10.1016/j.ijid.2020.05.048 doi: 10.1016/j.ijid.2020.05.048 id: cord-258078-k7y8k1vx author: Jang, Sukbin title: Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy date: 2020-05-26 words: 1475.0 sentences: 92.0 pages: flesch: 50.0 cache: ./cache/cord-258078-k7y8k1vx.txt txt: ./txt/cord-258078-k7y8k1vx.txt summary: title: Three cases of treatment with Nafamostat in elderly patients with COVID-19 pneumonia who need oxygen therapy We report three cases of COVID-19 pneumonia who progressed while using antiviral drugs and needed supplementary oxygen therapy, improved after treatment with nafamostat. Three COVID-19 patients had the following conditions: pneumonia with progression despite antiviral treatment; were elderly, over 65 years; and had underlying diseases that were known as high risk J o u r n a l P r e -p r o o f factors. On admission, he was not dyspneic or cyanotic, with a body temperature of 37.0°C, respiratory rate of 20 breaths per minute, heart rate of 75 beats per minute, and blood pressure of 140/90 mmHg. Initial laboratory results were as follows: white blood cell (WBC) count 5,150/μL (65% segmented neutrophil), and C-reactive protein (CRP) 2.61 mg/dL. abstract: No effective treatment for COVID-19 has been well established yet. Nafamostat, known as anticoagulant, has potential anti-inflammatory and anti-viral activities against COVID-19. We report three cases of COVID-19 pneumonia who progressed while using antiviral drugs and needed supplementary oxygen therapy, improved after treatment with nafamostat. These preliminary findings show the possibility that Nafamostat can be considered to be used in elderly patients with COVID-19 pneumonia who need oxygen therapy. The effectiveness of nafamostat should be evaluated in further studies. url: https://www.sciencedirect.com/science/article/pii/S1201971220303799?v=s5 doi: 10.1016/j.ijid.2020.05.072 id: cord-315860-9j667c03 author: Jullien, Sophie title: Pneumonia in children admitted to the national referral hospital in Bhutan: A prospective cohort study date: 2020-04-10 words: 5633.0 sentences: 300.0 pages: flesch: 45.0 cache: ./cache/cord-315860-9j667c03.txt txt: ./txt/cord-315860-9j667c03.txt summary: METHODS: This prospective study enrolled children aged 2–59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital with World Health Organization (WHO)-defined clinical pneumonia. CONCLUSION: Respiratory viral infections predominated among this cohort of WHO-defined clinical pneumonia cases, whereas bacterial aetiologies were uncommon, highlighting the epidemiologic transition that Bhutan seems to have reached. We conducted this prospective hospital-based observational study to describe the epidemiology, aetiology, and clinical and radiological presentation of World Health Organization (WHO)defined pneumonia among children aged between 2 and 59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital in Thimphu. All children aged 2-59 months hospitalized with WHO-defined pneumonia (irrespective of severity) were eligible for recruitment (World Health Organization, 2014) (see Box 1). Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study abstract: OBJECTIVES: The study aim was to describe the etiological profile and clinical characteristics of pneumonia among children hospitalized in Thimphu, Bhutan. METHODS: This prospective study enrolled children aged 2–59 months admitted to the Jigme Dorji Wangchuck National Referral Hospital with World Health Organization (WHO)-defined clinical pneumonia. Demographic and clinico-radiological data were collected through questionnaires, physical examination, and chest radiography. Blood samples and nasopharyngeal washing were collected for microbiological analysis including culture and molecular methods. RESULTS: From July 2017 to June 2018, 189 children were enrolled, of which 53.4% were infants. Pneumonia-related admissions were less frequent over the winter. Chest radiographies were obtained in 149 children; endpoints included pneumonia in 39 cases (26.2%), other infiltrates in 31 (20.8%), and were normal in 79 children (53.0%). Non-contaminated bacterial growth was detected in 8/152 (5.3%) blood cultures, with only two cases of Streptococcus pneumoniae. Viral detection in upper respiratory secretions was common, with at least one virus detected in 103/115 (89.6%). The three most-commonly isolated viruses were respiratory syncytial virus (52/115; 45.2%), rhinovirus (42/115; 36.5%), and human parainfluenza virus (19/115; 16.5%). A third of patients with viral infections showed mixed infections. Case fatality rate was 3.2% (6/189). CONCLUSION: Respiratory viral infections predominated among this cohort of WHO-defined clinical pneumonia cases, whereas bacterial aetiologies were uncommon, highlighting the epidemiologic transition that Bhutan seems to have reached. url: https://www.sciencedirect.com/science/article/pii/S1201971220302332 doi: 10.1016/j.ijid.2020.04.017 id: cord-259837-5tbdqzxr author: Kalcioglu, Mahmut Tayyar title: May COVID-19 cause sudden sensorineural hearing loss? date: 2020-09-29 words: 519.0 sentences: 38.0 pages: flesch: 59.0 cache: ./cache/cord-259837-5tbdqzxr.txt txt: ./txt/cord-259837-5tbdqzxr.txt summary: title: May COVID-19 cause sudden sensorineural hearing loss? In previous studies, viral infections have been reported to have an important role in the etiology of sudden sensorineural hearing loss (SSNHL) (Cohen et al., 2014) . Moreover, recently, studies on the effects of SARS-CoV-2 virus on central and peripheral nervous systems have been published. Some of these studies have reported Guillain -Barré syndrome (Toscano et al., 2020) and impaired olfactory function (Eliezer et al., 2020) to be related to SARS-CoV-2. Another recently published study reported neurologic changes in 58 of 64 patients with COVID-19 (Helms et al., 2020) . Therefore, we investigated the possibility of SARS-CoV-2 infection in these J o u r n a l P r e -p r o o f patients. Sudden and Complete Olfactory Loss Function as a Possible Symptom of COVID-19 An investigation into SARS-COV-2 in the etiology of sudden sensorineural hearing loss abstract: nan url: https://doi.org/10.1016/j.ijid.2020.09.1468 doi: 10.1016/j.ijid.2020.09.1468 id: cord-268389-0agwvsrv author: Kaminski, Monica A. title: Tocilizumab Therapy of COVID-19: A Comparison of Subcutaneous and Intravenous Therapies date: 2020-09-28 words: 3409.0 sentences: 184.0 pages: flesch: 47.0 cache: ./cache/cord-268389-0agwvsrv.txt txt: ./txt/cord-268389-0agwvsrv.txt summary: This study aimed to compare the effects of intravenous (IV) and subcutaneous (SC) tocilizumab, an IL-6 receptor antagonist, on respiratory parameters and clinical outcome in patients with COVID 19. C-reactive protein levels were significantly higher in patients in the IV group that did not respond (Table 2) Lastly, laboratory markers of inflammation were analyzed before and during the seven days following tocilizumab therapy to identify trends that correlated with response involving the respiratory parameters (Table 3) . Tocilizumab has been found to be associated with improved outcomes in patients with COVID-19 related respiratory disease, particularly for patients with critical illness (i.e., requiring mechanical ventilation) (Rossotti et al., 2020 , Somers et al., 2020 . In our report, levels of C-reactive protein fell acutely in both patients that did and did not have improvement in respiratory parameters seven days following tocilizumab therapy. abstract: Background The release of pro-inflammatory cytokines, resulting in cytokine storm syndrome, contributes to the morbidity and mortality associated with COVID-19 disease. This study aimed to compare the effects of intravenous (IV) and subcutaneous (SC) tocilizumab, an IL-6 receptor antagonist, on respiratory parameters and clinical outcome in patients with COVID 19. Methods We performed a retrospective cohort study of hospitalized patients with COVID-19 treated with either IV or SC tocilizumab from March 26, 2020 to May 18, 2020. Respiratory parameters seven days after receiving tocilizumab therapy were compared to baseline measurements. All patients were assessed until discharged from the hospital. Results Tocilizumab was administered to 125 patients: 65 received IV and 60 received SC therapy. At day seven, 52% of the patients in the IV group demonstrated improvement in respiratory parameters, compared to 28% in the SC group (P = 0.01). Mortality rates at days seven and 28 were 15% and 37%, respectively in the IV group and 17% and 50%, respectively in the SC group (P = NS). In-hospital mortality rate was 38% for the IV group versus 57% for the SC group (P = 0.04). More than 90% of patients in each group received corticosteroids, however significantly more patients in received convalescent plasma in the IV group. Conclusions At the doses used in this study, IV tocilizumab is preferred over SC therapy for the treatment of cytokine storm syndrome due to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33002613/ doi: 10.1016/j.ijid.2020.09.1447 id: cord-291638-oatrjbo3 author: Kang, Dayun title: Spatial epidemic dynamics of the COVID-19 outbreak in China date: 2020-04-03 words: 2637.0 sentences: 160.0 pages: flesch: 59.0 cache: ./cache/cord-291638-oatrjbo3.txt txt: ./txt/cord-291638-oatrjbo3.txt summary: This study described the spatio-temporal pattern and measured the spatial association of the early stages of the COVID-19 epidemic in mainland China from 16 January–06 February 2020. The results showed that most of the models, except medical-care-based connection models, indicated a significant spatial association of COVID-19 infections from around 22 January 2020. There are 31 provinces in mainland China, and this study used 3 weeks'' data from 16 January to 06 February 2020, which was during the early stages of COVID-19 in China. Because COVID-19 spread from Hubei Province, the epicentre of the outbreak, the number of newly confirmed cases in the provinces neighbouring Hubei was investigated. It used Moran''s I statistic, a measure of spatial association, for the number of confirmed cases with different types of neighbourhoods. On 22 January Models 1-4 first detected a significant spatial dependency on the number of newly confirmed cases. Since approximately 24 January, the number of newly confirmed cases show significant spatial dependency in Models 1 and 2. abstract: BACKGROUND: On 31 December 2019 an outbreak of COVID-19 in Wuhan, China, was reported. The outbreak spread rapidly to other Chinese cities and multiple countries. This study described the spatio-temporal pattern and measured the spatial association of the early stages of the COVID-19 epidemic in mainland China from 16 January–06 February 2020. METHODS: This study explored the spatial epidemic dynamics of COVID-19 in mainland China. Moran’s I spatial statistic with various definitions of neighbours was used to conduct a test to determine whether a spatial association of the COVID-19 infections existed. RESULTS: The spatial spread of the COVID-19 pandemic in China was observed. The results showed that most of the models, except medical-care-based connection models, indicated a significant spatial association of COVID-19 infections from around 22 January 2020. CONCLUSIONS: Spatial analysis is of great help in understanding the spread of infectious diseases, and spatial association was the key to the spatial spread during the early stages of the COVID-19 pandemic in mainland China. url: https://www.ncbi.nlm.nih.gov/pubmed/32251789/ doi: 10.1016/j.ijid.2020.03.076 id: cord-351740-779g8tr1 author: Khaba, Moshawa Calvin title: COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date: 2020-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite measures put in places to curb the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across South Africa, there has been a rapid spread which caused extensive morbidity and mortality. Whilst there is currently increased COVID-19 associated death, autopsies on COVID positive individuals are not routinely performed. An autopsy was performed on a 19 years old African patient who was recently diagnosed with human immunodeficiency virus (HIV). He presented with clinical features of SARS-CoV-2 which subsequently tested positive for. Important histopathological findings included diffuse alveolar damage and fibrin thrombi. No superimposed infections were noted. The cause of death was attributed to COVID-19. We report the first autopsy case of HIV-infected individual with COVID-19 as the cause of death. url: https://doi.org/10.1016/j.ijid.2020.09.1435 doi: 10.1016/j.ijid.2020.09.1435 id: cord-321412-6g3obmzc author: Khamis, Faryal title: Therapeutic Plasma Exchange in Adults with Severe COVID-19 Infection date: 2020-06-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To evaluate the therapeutic use of plasma exchange in COVID-19 patients compared to controls. METHODS: Case series of critically ill adult men and non-pregnant women, ≥18 years of age, with laboratory confirmed COVID-19, was conducted at the Royal Hospital, Oman, from April 17(th) to May 11(th), 2020. Therapeutic plasma exchange (TPE) was performed on patients admitted to intensive care unit (ICU) with confirmed or imminent acute respiratory distress syndrome (ARDS) or severe pneumonia. Analysis was performed using univariate statistics. RESULTS: A total of 31 COVID-19 patients were included with an overall mean age of 51 ± 15 years (range: 27-76 years), 90% (n = 28) were males, and 35% (n = 11) of the patients had TPE as a mode of treatment. The TPE group was associated with higher extubation rates than the non-TPE cohort (73% versus 20%; p = 0.018). Additionally, patients on TPE had a lower 14 days (0 versus 35%; p = 0.033) and 28 days (0 versus 35%; p = 0.033) all-cause mortality compared to patients not on TPE. However, all-cause mortality was only marginally lower in the TPE group compared to the non-TPE group (9.1% versus 45%; p = 0.055; power = 66%). Laboratory and ventilatory parameters also improved with the TPE. CONCLUSIONS: The use of TPE in severe COVID-19 patients has been associated with improved outcomes, however, randomized controlled clinical trials are warranted to draw final conclusive findings. url: https://www.sciencedirect.com/science/article/pii/S1201971220304999?v=s5 doi: 10.1016/j.ijid.2020.06.064 id: cord-261672-0cresfn8 author: Kim, Sungchan title: Evaluation of COVID-19 epidemic outbreak caused by temporal contact-increase in South Korea date: 2020-05-14 words: 1635.0 sentences: 108.0 pages: flesch: 59.0 cache: ./cache/cord-261672-0cresfn8.txt txt: ./txt/cord-261672-0cresfn8.txt summary: OBJECTIVES: On March 15, 2020, 61.3% of the confirmed cases of COVID-19 infection are associated with the worship service that was organized on February 9 in the Shincheonji Church of Jesus in Daegu, South Korea. METHOD: Using opened data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model. The effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on February 9 in the Shincheonji Church of Jesus, Daegu. However, the effective reproduction number decreased to less than unity after February 28 owing to the implementation of high-level preventive control interventions in South Korea, coupled with voluntary prevention actions by citizens. In this study, we aimed to evaluate the effects of mass infection due to temporal increases in contacts and assess the preventive control interventions using the confirmed cases and deaths data associated with COVID-19 in Korea. abstract: OBJECTIVES: On March 15, 2020, 61.3% of the confirmed cases of COVID-19 infection are associated with the worship service that was organized on February 9 in the Shincheonji Church of Jesus in Daegu, South Korea. In this study, we aim to evaluate the effects of mass infection in South Korea and assess the preventive control intervention. METHOD: Using opened data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model. RESULTS: The basic reproduction number was estimated to be [Formula: see text]. The effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on February 9 in the Shincheonji Church of Jesus, Daegu. However, the effective reproduction number decreased to less than unity after February 28 owing to the implementation of high-level preventive control interventions in South Korea, coupled with voluntary prevention actions by citizens. CONCLUSION: Preventive action and control intervention were fairly established in South Korea. url: https://www.ncbi.nlm.nih.gov/pubmed/32417246/ doi: 10.1016/j.ijid.2020.05.036 id: cord-259501-iggw1exl author: Kim, Yong Yean title: Acute Respiratory Illness in Rural Haiti date: 2019-02-14 words: 4623.0 sentences: 227.0 pages: flesch: 54.0 cache: ./cache/cord-259501-iggw1exl.txt txt: ./txt/cord-259501-iggw1exl.txt summary: Earlier studies in resource-poor settings have identified Streptococcus pneumoniae, Haemophilus influenzae type B and Staphylococcus aureus as important bacterial causes of ARI, and respiratory syncytial virus (RSV) and Influenza as important viral causes (Rudan et al., 2008) . A multicountry study that included Haiti showed that agents detected in hospitalized children less than 5 years of age who had pneumonia included RSV, Influenza A and B, Parainfluenza viruses, Adenovirus and Human metapneumovirus (HMPV) (Bénet et al., 2017) . Analysis of specific viral or bacterial agents detected showed more children with FluA or FluB had LRTI (33%) compared to URTI (15%) [ Table 5 ]. The overall findings of RV as the most common virus detected followed by Influenza in Haiti is comparable to that found in studies of children in other tropical, resource-poor countries (Hoffman et al., 2012; Schlaudecker et al., 2012; Taylor et al., 2017) . abstract: OBJECTIVES: Acute Respiratory Infection (ARI) is the most common cause of childhood morbidity and mortality in developing countries, including Haiti. Our objective was to detect pathogens found in children with ARI in rural Haiti to help develop evidence-based guidelines for treatment and prevention. METHODS: Retrospective study of students with ARI at four schools in rural Haiti. Viral and/or bacterial pathogens were identified by qPCR in 177 nasal swabs collected from April 2013 through November 2015. RESULTS: Most common viruses detected were Rhinovirus (36%), Influenza A (16%) and Adenovirus (7%), and bacteria were Streptococcus pneumoniae (58%) and Staphylococcus aureus (28%). Compared to older children, children aged 3–5 years had more Influenza A (28% vs. 9%, p = 0.002) and Adenovirus detected (14% vs. 3%, p = 0.01). Similarly, S. pneumoniae was greatest in children 3–5 years old (71% 3–5yrs; 58% 6–15 years; 25% 16–20 years; p = 0.008). Children 3–10 years old presented with fever more than children 11–20 years old (22% vs 7%; p = 0.02) and were more often diagnosed with pneumonia (28% vs 4%, p < 0.001). CONCLUSIONS: Younger children had increased fever, pneumonia, and detection of Influenza A and S. pneumoniae. These data support the need for influenza and pneumococcus vaccination in early childhood in Haiti. url: https://api.elsevier.com/content/article/pii/S1201971219300670 doi: 10.1016/j.ijid.2019.02.003 id: cord-311453-l6quzef6 author: Klopfenstein, Timothée title: Impact of Tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 COVID-19 patients date: 2020-08-13 words: 2675.0 sentences: 154.0 pages: flesch: 55.0 cache: ./cache/cord-311453-l6quzef6.txt txt: ./txt/cord-311453-l6quzef6.txt summary: CONCLUSION: Despite the small sample size in the group TCZ, this result suggests that TCZ reduces mortality and/or IMV requirement in patients with severe SARS-CoV-2 pneumonia. We have recently published a retrospective study including 45 patients treated in our hospital, which shows that TCZ seems to reduce the number of COVID-19 severe cases and/or mortality (11) . Based on the medical literature, we checked several criteria before starting TCZ treatment: no contraindication to TCZ, confirmed COVID-19 with real-time reverse transcription (RT)-PCR SARS-CoV-2 RNA, failure of standard treatment, period since symptoms onset ≥ 5 days, oxygen therapy ≥ 4 liters/min, ≥ 25% of lung damages on chest computed tomography (CT) scan, and ≥ 2 parameters of inflammation or biological markers of mortality (with a high level) such as ferritin, CRP, D-dimer, lymphopenia, and/or lactate dehydrogenase. abstract: INTRODUCTION: No therapy has proven to be effective yet to reduce mortality and/or invasive mechanical ventilation (IMV) requirement in COVID-19. Tocilizumab (TCZ) in patients with severe COVID-19 could be an effective treatment. METHOD: We conducted a retrospective case-control study in the Nord Franche-Comté Hospital, France. We compared the outcome of patients treated with TCZ and patients without TCZ considering a combined primary endpoint: mortality and/or IMV requirement. RESULTS: Thirty patients were treated with TCZ and 176 patients were treated without TCZ. TCZ was used in patients in a critical condition (oxygen therapy flow at TCZ onset was 10.5 l/min and 14/30 patients had ≥ 50% lung involvement on CT scan) as a rescue treatment (8/30 patients who died were not admitted in USC in regards to their comorbidities). However, mortality and/or IMV requirement were lower in patients with TCZ than in patients without TCZ (27% vs 52%, p = 0.009). CONCLUSION: Despite the small sample size in the group TCZ, this result suggests that TCZ reduces mortality and/or IMV requirement in patients with severe SARS-CoV-2 pneumonia. This notion needs to be confirmed and spread in the medical community. url: https://api.elsevier.com/content/article/pii/S1201971220306536 doi: 10.1016/j.ijid.2020.08.024 id: cord-300583-0krbrj4w author: Koh, Wee Chian title: Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis date: 2020-08-13 words: 3743.0 sentences: 207.0 pages: flesch: 52.0 cache: ./cache/cord-300583-0krbrj4w.txt txt: ./txt/cord-300583-0krbrj4w.txt summary: METHODS: We identified three distinct physical distancing measures with varying intensity and implemented at different times—international travel controls, restrictions on mass gatherings, and lockdown-type measures—based on the Oxford COVID-19 Government Response Tracker. INTERPRETATION: A combination of physical distancing measures, if implemented early, can be effective in containing COVID-19—tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak. is the average reproduction number of country over the 14 days following the date of the 100 th case; is country ''s physical distancing measure of type on the date of the 100 th case; represents the country characteristic (income level, population density, age structure, and temperature) of country ; is a constant term, ''s are the regression coefficients, and denotes the error term. abstract: BACKGROUND: Epidemic modelling studies predict that physical distancing is critical in containing COVID-19. However, few empirical studies have validated this finding. Our study evaluates the effectiveness of different physical distancing measures in controlling viral transmission. METHODS: We identified three distinct physical distancing measures with varying intensity and implemented at different times—international travel controls, restrictions on mass gatherings, and lockdown-type measures—based on the Oxford COVID-19 Government Response Tracker. We also estimated the time-varying reproduction number (R(t)) for 142 countries and tracked R(t) temporally for two weeks following the 100th reported case in each country. We regressed R(t) on the physical distancing measures and other control variables (income, population density, age structure, and temperature) and performed several robustness checks to validate our findings. FINDINGS: Complete travel bans and all forms of lockdown-type measures have been effective in reducing average R(t) over the 14 days following the 100th case. Recommended stay-at-home advisories and partial lockdowns are as effective as complete lockdowns in outbreak control. However, these measures have to be implemented early to be effective. Based on the observed median timing across countries worldwide, lockdown-type measures are considered early if they were instituted about two weeks before the 100th case and travel bans a week before detection of the first case. INTERPRETATION: A combination of physical distancing measures, if implemented early, can be effective in containing COVID-19—tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak. url: https://doi.org/10.1016/j.ijid.2020.08.026 doi: 10.1016/j.ijid.2020.08.026 id: cord-304743-0bsdahh6 author: Kortepeter, Mark G title: Marburg Virus Disease: a Summary for Clinicians date: 2020-08-03 words: 1327.0 sentences: 92.0 pages: flesch: 43.0 cache: ./cache/cord-304743-0bsdahh6.txt txt: ./txt/cord-304743-0bsdahh6.txt summary: Abstract Objectives This article is a summary of countermeasures for Marburg virus disease focusing on pathogenesis, clinical features, and diagnostics, with an emphasis on therapies and vaccines that have demonstrated potential for use in an emergency situation, through their evaluation in nonhuman primates (NHPs) and/or in humans. Results We identified six treatments and four vaccine platforms that have demonstrated potential benefit for treating or preventing infection in humans, through their efficacy in NHPs. Conclusion We provide succinct summaries of Marburg countermeasures to give the busy clinician a head start in reviewing the literature if faced with a patient with Marburg virus disease. Postexposure protection against Marburg haemorrhagic fever with recombinant vesicular stomatitis virus vectors in non-human primates: an efficacy assessment Vesicular stomatitis virus-based vaccines protect nonhuman primates against aerosol challenge with Ebola and Marburg viruses. Single-injection vaccine protects nonhuman primates against infection with Marburg virus and three species of ebola virus abstract: Abstract Objectives This article is a summary of countermeasures for Marburg virus disease focusing on pathogenesis, clinical features, and diagnostics, with an emphasis on therapies and vaccines that have demonstrated potential for use in an emergency situation, through their evaluation in nonhuman primates (NHPs) and/or in humans. Methods A standardized literature review was conducted on vaccines and treatments for each pathogen, with a focus on human and nonhuman primate data published in the last five years. More detail on the methods used are summarized in a companion methods paper. Results We identified six treatments and four vaccine platforms that have demonstrated potential benefit for treating or preventing infection in humans, through their efficacy in NHPs. Conclusion We provide succinct summaries of Marburg countermeasures to give the busy clinician a head start in reviewing the literature if faced with a patient with Marburg virus disease. We also provide links to other authoritative sources of information. url: https://www.ncbi.nlm.nih.gov/pubmed/32758690/ doi: 10.1016/j.ijid.2020.07.042 id: cord-316505-tdlj5smv author: Kumar, Abhai title: Proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers date: 2013-11-28 words: 4494.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-316505-tdlj5smv.txt txt: ./txt/cord-316505-tdlj5smv.txt summary: METHODS: Proteomics-based studies were done to determine the expression of differentially expressed proteins in the plasma of controls, acute typhoid cases, and chronic typhoid carriers. Two-dimensional (2D) gel electrophoresis and mass spectrometry techniques were used to identify newer proteins that may provide an insight into the host-pathogen interactions after Salmonella infection and in further colonization of the host leading to the chronic typhoid carrier state. The expression of proprotein convertase subtilisin, haptoglobin, and albumin in chronic typhoid carriers was significantly higher compared to those of control and acute typhoid cases (p < 0.01 and p < 0.01, respectively; Figure 3 ). typhi infection in enteric fever cases using bacteriological and serological methods and used 2D gel electrophoresis and mass spectrometry as an alternative method to differentiate chronic typhoid carriers based on alterations in the expression of proteins. When analyzed, the plasma proteome of controls, acute typhoid cases, and chronic typhoid carriers showed significant differences in the expression of four protein spots. abstract: BACKGROUND: Current diagnostic tests are inadequate to detect typhoid cases, as well as the chronic carrier state, the sole reservoir of Salmonella enterica serovar Typhi. The current study was conducted to find new molecular signatures of pathogen/disease to understand the mechanism behind the host–pathogen interaction in enteric fever. METHODS: Proteomics-based studies were done to determine the expression of differentially expressed proteins in the plasma of controls, acute typhoid cases, and chronic typhoid carriers. Further, transcriptome-based analysis using reverse-transcriptase PCR (RT-PCR) was done in controls, acute typhoid cases, and chronic typhoid carriers. RESULTS: Results showed the upregulation of proprotein convertase subtilisin, furin, haptoglobin, and albumin in the plasma of chronic typhoid carriers. The elevation in mRNA expression of four differentially expressed proteins confirms the changes at the transcriptional level. Further, the increase in albumin and haptoglobin in chronic typhoid carriers shows their role in free radical generation, inflammation, and monocyte cell signaling. CONCLUSION: Through proteomics techniques, this study identified four proteins in the chronic typhoid carrier host that may have a role in the disease pathogenesis of enteric fever. url: https://api.elsevier.com/content/article/pii/S120197121300338X doi: 10.1016/j.ijid.2013.10.008 id: cord-305763-160heazx author: Lai, Chih-Cheng title: Population-based seroprevalence surveys of anti-SARS-CoV-2 antibody: An up-to-date review date: 2020-10-09 words: 4257.0 sentences: 264.0 pages: flesch: 61.0 cache: ./cache/cord-305763-160heazx.txt txt: ./txt/cord-305763-160heazx.txt summary: One population-based study demonstrated that the positive rate of anti-SARS-CoV-2 IgG or IgM in the J o u r n a l P r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . Many studies had evaluated the seroprevalence among HCWs (Steensels et al., 2020; Martin et al., 2020; Korth et al., 2020; Stubblefield et al., 2020; Pallett et al., 2020; Grant et al., 2020; Hunter et al., 2020; Self et al., 2020; Moscola et al., 2020; Plebani et al., 2020 HCWs who regularly had direct contact with units housing adult COVID-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the SARS-CoV-2 spike protein (Stubblefield et al., 2020) . These findings may be due to the fact that anti-SARS-CoV-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the COVID-19 pandemic, and methods used for serology tests. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), has led to a global pandemic. However, the majority of currently available data are restricted to laboratory-confirmed cases for symptomatic patients, and the SARS-CoV-2 infection can manifest as an asymptomatic or mild disease; therefore, the true extent of the burden of COVID-19 can be underestimated. Improved serological detection of specific antibodies against SARS-CoV-2 can help estimate the true number of infections. This article comprehensively reviewed the associated literature and provides updated information regarding the seroprevalence of the anti-SARS-CoV-2 antibody. The seroprevalence can vary according to different sites and the seroprevalence can increase with time in the longitudinal follow-up. Although healthcare workers (HCWs), especially those caring for COVID-19 patients, are considered as a high-risk group, the seroprevalence of a HCW wearing adequate personal protective equipment is thought to not be higher than other groups. With regard to sex, no statistical difference has been found between male and female subjects. Some, but not all, studies have shown that children have a lower risk than other age groups. Finally, seroprevalence can vary according to different populations, such as pregnant women and hemodialysis patients; however, limited studies have examined these associations. Furthermore, continued seroprevalence surveillance is warranted to estimate and monitor the growing burden of COVID-19. url: https://doi.org/10.1016/j.ijid.2020.10.011 doi: 10.1016/j.ijid.2020.10.011 id: cord-286743-z0e5arlm author: Langer-Gould, Annette title: Early Identification of COVID-19 Cytokine Storm and Treatment with Anakinra or Tocilizumab date: 2020-08-06 words: 4258.0 sentences: 213.0 pages: flesch: 43.0 cache: ./cache/cord-286743-z0e5arlm.txt txt: ./txt/cord-286743-z0e5arlm.txt summary: Subsequently, a shift in practice by clinicians at some of our medical centers aimed to identify early COVID19-CS through laboratory abnormalities in patients with increasing O2 requirements and to initiate combined treatment with anakinra and corticosteroids occurred. Data were extracted by manual reviewing the EHR, including onset of dyspnea and other COVID-19 symptoms, age, sex, comorbidities, smoking status, tocilizumab and anakinra use, other J o u r n a l P r e -p r o o f treatments rendered for hydroxychloroquine, and/or corticosteroids) , fever (>100.4F), hypotension requiring pressors, dates of admission, intubation, extubation, discharge and/or death. The primary purpose of analyses was to describe clinical outcomes among tocilizumab-or anakinra-treated COVID-19 patients and to examine whether differences in outcomes could be accounted for by COVID19-CS severity and/or duration at the time of treatment initiation (baseline). abstract: OBJECTIVE: To examine outcomes among patients who were treated with the targeted anti-cytokine agents, anakinra or tocilizumab, for COVID-19 -related cytokine storm (COVID19-CS). METHODS: We conducted a retrospective cohort study of all SARS-coV2-RNA-positive patients treated with tocilizumab or anakinra in Kaiser Permanente Southern California. Local experts developed and implemented criteria to define COVID19-CS. All variables were extracted from the electronic health record. RESULTS: At tocilizumab initiation (n = 52), 50 (96.2%) were intubated, and only 7 (13.5%) received concomitant corticosteroids. At anakinra initiation (n = 41), 23 (56.1%) were intubated, and all received concomitant corticosteroids. Fewer anakinra-treated patients died (n = 9, 22%) and more were extubated/never intubated (n = 26, 63.4%) compared to tocilizumab-treated patients (n = 24, 46.2% dead, n = 22, 42.3% extubated/never intubated). Patients who died had more severe sepsis and respiratory failure and met COVID-CS laboratory criteria longer (median = 3 days) compared to those extubated/never intubated (median = 1 day). After accounting for differences in disease severity at treatment initiation, this apparent superiority of anakinra over tocilizumab was no longer statistically significant (propensity score-adjusted hazards ratio 0.46, 95% confidence interval 0.18–1.20). CONCLUSIONS: Prompt identification and treatment of COVID19-CS prior to intubation may be more important than the specific type of anti-inflammatory treatment. Randomized controlled trials of targeted anti-cytokine treatments and corticosteroids should report duration of cytokine storm in addition to clinical severity at randomization. url: https://api.elsevier.com/content/article/pii/S1201971220306093 doi: 10.1016/j.ijid.2020.07.081 id: cord-008219-ng9xb46c author: Lassmann, Britta title: Highlights from the 6(th) International Meeting on Emerging Diseases and Surveillance (IMED 2016) Vienna, Austria from Nov 3 to 7, 2016 date: 2016-12-09 words: 2518.0 sentences: 131.0 pages: flesch: 47.0 cache: ./cache/cord-008219-ng9xb46c.txt txt: ./txt/cord-008219-ng9xb46c.txt summary: c o m / l o c a t e / i j i d During the oral abstract presentation session on One Health -Diseases Across Species Boundaries, Toph Allen from EcoHealth Alliance and colleagues shared results from an updated model assessing the global distribution of zoonotic emerging infectious disease risk. Professor [ 1 7 _ T D $ D I F F ] Daniel Lucey summarized the commissions'' recommendations including the importance of strengthening national health systems, consolidating and strengthening World Health Organization (WHO) emergency and outbreak response activities, and enhancing research and development. In a separate session, the challenges posed by climate change on infectious disease outbreaks and how to best prevent and track diseases in mobile populations were discussed. The importance of the food chain as a source for emergence and spread of antimicrobial resistance between animals and humans was highlighted in a nation-wide study in Lebanon. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129744/ doi: 10.1016/j.ijid.2016.12.008 id: cord-276445-m5vjo3ym author: Lee, Hyojung title: Recrudescence of Ebola virus disease outbreak in West Africa, 2014–2016 date: 2017-09-20 words: 1632.0 sentences: 88.0 pages: flesch: 54.0 cache: ./cache/cord-276445-m5vjo3ym.txt txt: ./txt/cord-276445-m5vjo3ym.txt summary: For the Ebola virus disease (EVD) outbreak in West Africa from 2014 to 2016, the World Health Organization (WHO) recommended securing 42 days (World Health Organization, 2015) , or twice the observed maximum incubation period, from the time at which the last case was found negative for the virus at second testing. WHO reports and other sources were reviewed in an analysis of all known recrudescence events occurring from 2014 to 2016 (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . A total of five cases of recrudescence were identified ( Figure 1 ): three occurred in Liberia and one each in Guinea and Sierra Leone (World Health Organization, 2016; Sheri, 2015; Farge and Giahyue, 2015; Dahl et al., 2016; Dakaractu, 2016; Center for Infectious Disease Research and Policy, 2016) . abstract: OBJECTIVES: There have been errors in determining the end of the Ebola virus disease (EVD) epidemic when adhering to the criteria of the World Health Organization. The present study aimed to review and learn from all known recrudescence events in West Africa occurring in 2014–2016. METHODS: Background mechanisms of five erroneous declarations in Guinea, Liberia, and Sierra Leone during 2014–2016 were reviewed. RESULTS: Three cases of recrudescence were suspected to have been caused by sexual contact with survivors, one to be due to international migration, and one was linked to a potentially immunocompromised mother. The three sexual transmission events involving survivors—the first two in Liberia and one in Sierra Leone—required 164 days, >150 days, and approximately 180 days, respectively, from discharge of the survivors to confirmation of the recrudescent case. CONCLUSIONS: The events of recrudescence were associated with relatively uncommon routes of transmission other than close contact during burial or care-giving, including sexual transmission, possible immunocompromise, and migration. Recognition of the sexual transmission risk among survivors could potentially involve discrimination, which may lead to under-ascertainment. url: https://api.elsevier.com/content/article/pii/S1201971217302370 doi: 10.1016/j.ijid.2017.09.013 id: cord-349645-6o8773c5 author: Li, He title: Air Pollution and temperature are associated with increased COVID-19 incidence: a time series study date: 2020-06-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Although the COVID-19 is known to cause by human-to-human transmission, it remains largely unclear whether ambient air pollutants and meteorological parameters could promote its transmission. METHODS: A retrospective study is conducted to study whether air quality index (AQI), four ambient air pollutants (PM(2.5), PM(10), NO(2) and CO) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase COVID-19 incidence in Wuhan and XiaoGan between Jan 26(th) to Feb 29(th) in 2020. RESULTS: First, a significant correlation was found between COVID-19 incidence and AQI in both Wuhan (R(2) = 0.13, p < 0.05) and XiaoGan (R(2) = 0.223, p < 0.01). Specifically, among four pollutants, COVID-19 incidence was prominently correlated with PM(2.5) and NO(2) in both cities. In Wuhan, the tightest correlation was observed between NO(2) and COVID-19 incidence (R(2) = 0.329, p < 0.01). In XiaoGan, in addition to the PM(2.5) (R(2) = 0.117, p < 0.01) and NO(2) (R(2) = 0.015, p < 0.05), a notable correlation was also observed between the PM(10) and COVID-19 incidence (R(2) = 0.105, p < 0.05). Moreover, temperature is the only meteorological parameter that constantly correlated well with COVID-19 incidence in both Wuhan and XiaoGan, but in an inverse correlation (p < 0.05). CONCLUSIONS: AQI, PM(2.5), NO(2), and temperature are four variables that could promote the sustained transmission of COVID-19. url: https://api.elsevier.com/content/article/pii/S1201971220303830 doi: 10.1016/j.ijid.2020.05.076 id: cord-275866-m89hgf41 author: Li, Ping title: Clinical Features and Short-term Outcomes of Elderly Patients With COVID-19 date: 2020-05-31 words: 2359.0 sentences: 145.0 pages: flesch: 55.0 cache: ./cache/cord-275866-m89hgf41.txt txt: ./txt/cord-275866-m89hgf41.txt summary: Methods 204 elderly patients (≥60 years old) diagnosed with COVID-19 in Renmin Hospital of Wuhan University from January 31st to February 20th, 2020 were included in this study. Multivariate analysis showed that dyspnea (hazards ratio (HR) 2.2, 95% confidence interval (CI) 1.414 to 3.517;p < 0.001), older age (HR 1.1, 95% CI 1.070 to 1.123; p < 0.001), neutrophilia (HR 4.4, 95% CI 1.310 to 15.061; p = 0.017) and elevated ultrasensitive cardiac troponin I (HR 3.9, 95% CI 1.471 to 10.433; p = 0.006) were independently associated with death. Univariate analysis showed age of 70 years or older, comorbidity (hypertension, J o u r n a l P r e -p r o o f cardiovascular disease, COPD, chronic renal failure), onset of dyspnea, and several laboratory indices abnormalities were associated with poor outcome. This study suggests that the elderly patients of COVID-19 have a rapid course of the disease and a higher case fatality ratio. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China abstract: Abstract Background The outbreak of Coronavirus Disease 2019 (COVID-19) has become a global public health emergency. Methods 204 elderly patients (≥60 years old) diagnosed with COVID-19 in Renmin Hospital of Wuhan University from January 31st to February 20th, 2020 were included in this study. Clinical endpoint was in-hospital death. Results Of the 204 patients, hypertension, diabetes, cardiovascular disease, and chronic obstructive pulmonary disease (COPD) were the most common coexisting conditions. 76 patients died in the hospital. Multivariate analysis showed that dyspnea (hazards ratio (HR) 2.2, 95% confidence interval (CI) 1.414 to 3.517;p < 0.001), older age (HR 1.1, 95% CI 1.070 to 1.123; p < 0.001), neutrophilia (HR 4.4, 95% CI 1.310 to 15.061; p = 0.017) and elevated ultrasensitive cardiac troponin I (HR 3.9, 95% CI 1.471 to 10.433; p = 0.006) were independently associated with death. Conclusion Although so far the overall mortality of COVID-19 is relatively low, the mortality of elderly patients is much higher. Early diagnosis and supportive care are of great importance for the elderly patients of COVID-19. url: https://api.elsevier.com/content/article/pii/S120197122030415X doi: 10.1016/j.ijid.2020.05.107 id: cord-274845-pqvlh3eg author: Li, Yan title: Characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in Beijing date: 2020-05-07 words: 1341.0 sentences: 76.0 pages: flesch: 56.0 cache: ./cache/cord-274845-pqvlh3eg.txt txt: ./txt/cord-274845-pqvlh3eg.txt summary: Here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory virus infection. COVID-19 group (83.33%) had higher rate of pneumonia in chest CT scan than Flu A and B virus infection groups. There was no statistical difference in complete blood count parameters between Similar to what was reported in COVID-19 [9] , fever was the most common symptom in the respiratory virus infection patients. In this study, the ratio of fever and the highest temperature were higher in Flu A virus infection patients than in COVID-19 patients. And in this study, it showed that COVID-19 patients even had lower WBC count and neutrophil count than Flu A virus and RSV infection group. Also, it was reported that they had low lymphocyte count [9, 10] , but this study found that the lymphocyte count was higher in COVID-19 than in Flu A and B virus infection patients. abstract: Abstract Background Coronavirus disease 2019 (COVID-19) is spreading. Here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory virus infection. Methods Retrospectively collected patients with definite etiological results using nasal and pharyngeal swabs in fever clinic. Results Totally, 1860 patients were screened and 136 patients were enrolled. 72 (52.94%) of them were diagnosed as influenza (Flu) A virus infection. 32 (23.53%) of them were diagnosed as Flu B virus infection. 18 (13.24%) and 14 (10.29%) of them were diagnosed as COVID-19 and respiratory syncytial virus (RSV) infection respectively. COVID-19 group had a higher rate of contact with epidemic area within 14 days and clustering onset than other groups. Fever was the most common symptom in these patients. The ratio of fever and the highest temperature were higher in Flu A virus infection patients than in COVID-19 patients. COVID-19 patients had lower white blood cell count and neutrophil count than Flu A virus and RSV infection group, but higher lymphocyte count than Flu A and B virus infection groups. COVID-19 group (83.33%) had higher rate of pneumonia in chest CT scan than Flu A and B virus infection groups. Conclusions Influenza viruses accounted for a large proportion of respiratory virus infection even during the epidemic of COVID-19 in Beijing. No single symptom or laboratory finding was suggestive of specific respiratory virus, however, epidemic history was important for screening of COVID-19. url: https://doi.org/10.1016/j.ijid.2020.05.008 doi: 10.1016/j.ijid.2020.05.008 id: cord-318808-1cfwj5uq author: Li, Ying title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years date: 2020-06-12 words: 1656.0 sentences: 111.0 pages: flesch: 55.0 cache: ./cache/cord-318808-1cfwj5uq.txt txt: ./txt/cord-318808-1cfwj5uq.txt summary: title: Comparison of Hospitalized Patients with pneumonia caused by COVID-19 and influenza A in children under 5 years Abstract Background Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. Therefore, the aim of this study was to compare the different clinical Page 5 of 15 J o u r n a l P r e -p r o o f 5 presentations between patients with infected with COVID-19 pneumonia versus influenza A pneumonia, to provide some recommendations for their differential diagnosis. Our present study revealed that COVID-19 manifested as mild, severe pneumonia were less than influenza A patients. In conclusion, COVID-19 patients were mild not only in clinical symptoms but also in laboratory examinations which including lymphocyte, CRP, PCT, D-dimer in the children under 5 years. abstract: Abstract Background Since the outbreak of Coronavirus Disease 2019 (COVID-19) in Wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. However, it is also crucial for clinicians to differentiate COVID-19 from other respiratory infectious diseases, such as influenza viruses. Methods This was a retrospective study. Two group of COVID-19 patients (n=57) and influenza A patients (n=59) were enrolled. We analyzed and compared their clinical manifestations, imaging characteristics and treatments. Results The proportions of cough (70.2%), fever (54.4%) and gastrointestinal symptoms (14.1%) in COVID-19 patients were lower than those of influenza A patients (98.3%, P<0.001; 84.7%, P<0.001; and 35.6%, P=0.007; respectively). In addition, COVID-19 patients showed significantly lower levels of leukocytes (7.87 vs. 9.89×109/L, P=0.027), neutrophils (2.43 vs. 5.16×109/L, P<0.001), C-reactive protein (CRP; 3.7 vs. 15.1mg/L, P=0.001) and procalcitonin (PCT; 0.09 vs. 0.68mm/h, P<0.001), while lymphocyte levels (4.58 vs. 3.56×109/L; P=0.006) were significantly higher compared with influenza A patients. In terms of CT imaging, ground-glass opacification in chest CT was more common in COVID-19 patients than in influenza A patients (42.1% vs. 15%, P=0.032). In contrast, consolidation was more common in influenza A patients (25%) than that in COVID-19 patients (5.2%, P=0.025). Conclusion The clinical manifestations and laboratory tests of COVID-19 children are milder than those of influenza A children under 5 years. Additionally, imaging results more commonly presented as ground-glass opacities in COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S1201971220304628?v=s5 doi: 10.1016/j.ijid.2020.06.026 id: cord-332348-yi85sfks author: Liang, Yujie title: Neurosensory dysfunction: a diagnostic marker of early COVID-19 date: 2020-06-29 words: 2748.0 sentences: 172.0 pages: flesch: 56.0 cache: ./cache/cord-332348-yi85sfks.txt txt: ./txt/cord-332348-yi85sfks.txt summary: Recently, some researchers have reported that patients with COVID-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for J o u r n a l P r e -p r o o f hypogeusia. To clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of In this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with COVID-19. In this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with COVID-19. In conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with COVID-19. abstract: Abstract Objectives To detailly described the neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, in patients with COVID-19. Methods Clinical characteristics and oropharyngeal swabs were obtained from 86 patients with COVID-19 hospitalized in Guangzhou Eighth People’s Hospital. Chronological analysis method was used to detailly clarify the neurosensory dysfunction. The cycle threshold (Ct) values were used to approximately indicate viral load. Results Forth-four (51.2%) patients had neurosensory dysfunction: hyposmia (34, 39.5%), hypogeusia (33, 38.4%), and tinnitus (3, 3.5%). Neurosensory dysfunction was significantly more common in patients under 40 years old (p = 0.001) or women (p = 0.006). Hyposmia and hypogeusia coexisted in 23 (26.7%) patients. The interval between onset of hyposmia and hypogeusia was 0.7 ± 1.46 days. The interval from onset of hyposmia and hypogeusia to typical symptoms was 0.22 ± 4.57 and 0.75 ± 6.77 days; the interval from onset of hyposmia and hypogeusia to admission was 6.06 ± 6.68 and 5.76 ± 7.68 days; and the duration of hyposmia and hypogeusia was 9.09 ± 5.74 and 7.12 ± 4.66 days, respectively. The viral load was high since symptoms onset, peaked within the first week, and then gradually declined. Conclusions The neurosensory dysfunction tends to occur in the early stage of COVID-19, and it could be used as a marker for early diagnosis of COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305191?v=s5 doi: 10.1016/j.ijid.2020.06.086 id: cord-290206-fmy4zrim author: Lim, Jue Tao title: The Costs of an Expanded Screening Criteria for COVID-19: A Modelling Study date: 2020-08-12 words: 4208.0 sentences: 203.0 pages: flesch: 47.0 cache: ./cache/cord-290206-fmy4zrim.txt txt: ./txt/cord-290206-fmy4zrim.txt summary: The screening process should therefore maximise sensitivity to minimise the number of missed cases and risk of nosocomial transmission, which occurred in Singapore during another coronavirus outbreak of Severe Acute Respiratory Syndrome (SARS) in 2003. Using ESC, NUH clinicians were able to identify and isolate 13 patients who did not fit the WHO SARS criteria but were eventually confirmed to have SARS, who would have otherwise been potential spreaders (the number of positive and negative cases for SARS are presented in Supplementary Table 1.) 12 Clinicians responded to the COVID-19 crisis similarly, implementing ESC on 7 th February 2020, which was approximately three weeks after the first imported case. At an of 2.5 and incubation period (IP) of 4 days, approximate to estimates by Wu and colleagues 29 for Wuhan, an estimated 240 (95% CI: 200-290) cases would be prevented over 150 days through ESC by isolating patients presenting fever or respiratory symptoms such as cough with their travel and exposure profile not considered (Table 2) . abstract: OBJECTIVES: Nosocomial infection is an ongoing concern in the COVID-19 outbreak. The effective screening of suspected cases in the healthcare setting is therefore necessary, enabling the early identification and prompt isolation of cases for epidemic containment. We aimed to assess the cost and health outcomes of an extended screening strategy, implemented in Singapore on 07 February 2020, which maximizes case identification in the public healthcare system. METHODS: We explored the effects of the expanded screening criteria which allows clinicians to isolate and investigate patients presenting with undifferentiated fever or respiratory symptoms or chest x-ray abnormalities. We formulated a cost appraisal framework which evaluated the treatment costs averted from the prevention of secondary transmission in the hospital setting, as determined by a branching process infection model, and compared these to the costs of the additional testing required to meet the criteria. RESULTS: In the base case analysis, an [Formula: see text] of 2.5 and incubation period of 4 days, an estimated 239 (95% CI: 201-287) cases could be averted over 150 days within the hospital setting through ESC. A corresponding $2.36 (2 – 2.85) million USD costs could be averted with net cost savings of $124 000 (95% CI: -334 000–516 000). In the sensitivity analyses, when positive identification rates (PIR) were above 7%, regardless of [Formula: see text] and incubation period, all scenarios were cost-saving. CONCLUSION: The expanded screening criteria can help to identify and promptly isolate positive COVID cases in a cost-saving manner or within acceptable cost margins where the costs incurred from the testing of negative patients could be negated by the averted costs. Outbreak control must be sustainable and effective; the proposed screening criteria should be considered to mitigate nosocomial transmission risk within healthcare facilities. url: https://api.elsevier.com/content/article/pii/S1201971220306548 doi: 10.1016/j.ijid.2020.08.025 id: cord-354780-yzyixucr author: Lin, Chih-Yen title: Importation of SARS-CoV-2 infection leads to major COVID-19 epidemic in Taiwan date: 2020-06-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Objective COVID-19 has recently become a pandemic affecting many countries worldwide. This study aims to evaluate current status of COVID-19 in Taiwan and analyze the source of infection. Methods National data regarding SARS-CoV-2 infection were obtained from Taiwan CDC at the end of April, 2020. These data were subjected for analysis of the current status and correlation between indigenous and imported COVID-19 cases. Phylogenetic tree was performed to analyze the phylogeny of Taiwanese SARS-CoV-2 isolates. Results The initial case of SARS-CoV-2 infection in Taiwan was detected on January 21, 2020. Epidemiological data indicate that by April 30, there were a total of 429 COVID-19 confirmed cases with the death rate of 1.3%. Most of cases were identified as imported (79.9%; 343/429) with majority transmitted from United States of America (22.1%) and United Kingdom (17.6%). Results from phylogenetic tree analyses indicate that the Taiwanese SARS-CoV-2 isolates were clustered with the SARS-CoV-2 isolates from other countries (bootstrap value 98%) and sub-clustered with bat SARS-like coronaviruses (bootstrap value 99%). Conclusion This study suggests that importation of SARS-CoV-2 infection was the primary risk-factor resulting in the COVID-19 epidemic in Taiwan. url: https://www.sciencedirect.com/science/article/pii/S1201971220304665?v=s5 doi: 10.1016/j.ijid.2020.06.031 id: cord-282177-8l7zukg4 author: Lin, Yi-Chun title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response date: 2020-05-26 words: 370.0 sentences: 31.0 pages: flesch: 55.0 cache: ./cache/cord-282177-8l7zukg4.txt txt: ./txt/cord-282177-8l7zukg4.txt summary: title: A case of transient existence of SARS-CoV-2 RNA in the respiratory tract with the absence of anti-SARS-CoV-2 antibody response ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths A case of COVID-19 and pneumonia returning from Macau in Taiwan: clinical course and anti-SARS-CoV-2 IgG dynamic Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 abstract: ABSTRACT We report a patient who had travelled to Japan presented mild respiratory symptom during the COVID-19 infection outbreak period. There was transient existence of SARS-CoV-2 RNA in his oropharynx. The RNA was absent in the six respiratory specimens that were subsequently tested. Anti-SARS-CoV-2 antibody response in the acute and convalescent sera were absent. The reported case indicates that transient colonization of SARS-CoV-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. url: https://api.elsevier.com/content/article/pii/S1201971220303775 doi: 10.1016/j.ijid.2020.05.070 id: cord-320785-42p8292o author: Lobo, Andréa de Paula title: COVID-19 epidemic in Brazil: where we at? date: 2020-06-16 words: 682.0 sentences: 55.0 pages: flesch: 70.0 cache: ./cache/cord-320785-42p8292o.txt txt: ./txt/cord-320785-42p8292o.txt summary: Abstract Objetive to analyze the trends of COVID-19 in Brazil in 2020 by Federal Units (FU). Joinpoint regression models were applied to identify points of inflection in COVID-19 trends, considering the days since the 50th confirmed case as time unit. Conclusions In summary, our results show that all FUs in Brazil present upward trends of COVID-19. Discussion: Although all FUs presented upward trends in the number of cumulative cases of COVID-19, 18 out of 27 FUs showed a reduction in the pace of the trend in the last segment. Even though the FUs from the Southeast region presented most of the confirmed cases, the highest ADPC values were found in the Northeast and North regions. (36.9;58.8) 3-11 13.8*(12.7;14.9) 11-20 8.1*(7.2;9.0 • All of Federative Units in Brazil shows a upward in accumulated cases of COVID-19. • Each Federative Unit in Brazil is at a different stage of the COVID-19 pandemic. abstract: Abstract Objetive to analyze the trends of COVID-19 in Brazil in 2020 by Federal Units (FU). Method ecological time-series based on cumulative confirmed cases of COVID-19 from March 11 to May 12. Joinpoint regression models were applied to identify points of inflection in COVID-19 trends, considering the days since the 50th confirmed case as time unit. Results Brazil reached the 50th confirmed case of COVID-19 in 11 March 2020 and, 63 days after that, on May 12, 177,589 cases had been confirmed. The trends for all regions and FU are upward. In the last segment, from the 31st to the 63rd day, Brazil presented a DPC of 7.3% (95%CI= 7.2;7.5). For the country the ADPC was 14.2% (95%CI: 13.8;14.5). The highest ADPC values were found in the North, Northeast and Southeast regions. Conclusions In summary, our results show that all FUs in Brazil present upward trends of COVID-19. In some FUs, the slowdown in DPC in the last segment must be considered carefully. Each FUs is at a different stage of the pandemic and, therefore, non-pharmacological measures must be applied accordingly. url: https://www.ncbi.nlm.nih.gov/pubmed/32561425/ doi: 10.1016/j.ijid.2020.06.044 id: cord-254776-m4makxr8 author: Luo, Shiua title: A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China date: 2020-06-01 words: 384.0 sentences: 32.0 pages: flesch: 62.0 cache: ./cache/cord-254776-m4makxr8.txt txt: ./txt/cord-254776-m4makxr8.txt summary: title: A Follow-up Study of Recovered Patients with COVID-19 in Wuhan, China The 2019 novel coronavirus disease (COVID-19) epidemic has clearly entered a new stage with rapid spread in countries outside China [1] . Currently, a large number of COVID-19 patients in Wuhan have been cured and discharged. In Wuhan, China, all cured patients with COVID-19 are required to quarantine in either a designated hotel room or at home for 14 days [3] . We retrospectively evaluated the data of the recovered patients with COVID-19 in two different designated fever clinics in Wuhan, with a goal to provide relevant information about these patients. In this study, only 7.7‰ patients experienced recurrence during isolation and observation, and all presented with mild symptoms. Serological tests to identify antibodies played a key role in surveillance of recurrence of COVID-19 [4] . Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220304264?v=s5 doi: 10.1016/j.ijid.2020.05.119 id: cord-323332-vu2cre8k author: Luo, Yang title: Factors impacting compliance with standard precautions in nursing, China date: 2010-11-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To evaluate registered nurse compliance with standard precautions and to analyze the factors that affect compliance. METHODS: Study data were collected over a 3-month period from June to September 2007. The survey research method was used. A total of 1500 randomly sampled registered nurses from 18 hospitals in Hunan, China completed self-report questionnaires. RESULTS: Of the 1500 nurses included in the study, 1444 returned valid self-report questionnaires. Compliance with standard precautions was found to be low in the surveyed nurses. With a maximum possible score of 80, the quartile range of the overall score for compliance for all nurses was 48.29 (upper quartile score 76.36, lower quartile score 28.07), which was occupied by 64.7% of the participants. The factors most affecting compliance were: standard precautions training (odds ratio (OR) 2.17, 95% confidence interval (CI) 1.85–2.55) and knowledge (OR 1.94, 95% CI 1.01–3.41), followed by hospital grade (OR 1.61, 95% CI 1.79–1.86), presence of sharps disposal box in the department (OR 1.43, 95% CI 1.10–3.41), general self-efficacy (OR 1.29, 95% CI 1.04–1.59), exposure experience (OR 0.69, 95% CI 0.56–0.85), and department in which the nurse worked (OR 1.24, 95% CI 1.05–1.46). CONCLUSIONS: The relevant authorities and hospital infection control department should pay more attention to nurse compliance with standard precautions. Standard precautions training should be strengthened and sufficient practical personal protection equipment provided in order to reduce hospital infections and protect the health of patients and medical staff. url: https://doi.org/10.1016/j.ijid.2009.03.037 doi: 10.1016/j.ijid.2009.03.037 id: cord-255021-acgfwjwi author: Luo, Ying title: Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus date: 2020-05-01 words: 595.0 sentences: 49.0 pages: flesch: 62.0 cache: ./cache/cord-255021-acgfwjwi.txt txt: ./txt/cord-255021-acgfwjwi.txt summary: title: Using the diagnostic model based on routine laboratory tests to distinguish patients infected with SARS-CoV-2 from those infected with influenza virus Abstract Background The differential diagnosis between novel coronavirus pneumonia patients (NCPP) and influenza patients (IP) remains a challenge in clinical practice. We observed that NCPP had significantly decreased white blood cells, alkaline phosphatase, and d-dimer, compared with IP. Conclusions Some routine laboratory results had statistical difference between NCPP and IP. A diagnostic model based on combination of routine laboratory results provides an adjunct approach in the differential diagnosis between NCPP and IP. We observed that NCPP had 37 significantly decreased white blood cells, alkaline phosphatase, and d-dimer, The Lancet, 2020). Epidemiological and clinical 307 characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a 308 descriptive study Clinical features of patients 312 infected with 2019 novel coronavirus in Wuhan abstract: Abstract Background The differential diagnosis between novel coronavirus pneumonia patients (NCPP) and influenza patients (IP) remains a challenge in clinical practice. Methods Between January 2018 and March 2020, 1027 NCPP and 1140 IP were recruited from Tongji hospital. Blood routine examination, biochemical indicators, and coagulation function analysis were performed in all participants simultaneously. Results There was no sex predominance in NCPP. The NCPP were frequently encountered in the sixth and seventh decades of life. The mean age of NCPP (56±16 years) was higher than IP (47±17 years), but without statistical difference. Although most results of routine laboratory tests between NCPP and IP had no significant difference, some laboratory tests showed an obvious change in NCPP. We observed that NCPP had significantly decreased white blood cells, alkaline phosphatase, and d-dimer, compared with IP. However, the results of lactate dehydrogenase, erythrocyte sedimentation rate and fibrinogen were significantly increased in NCPP compared with those in IP. The diagnostic model based on combination of eighteen routine laboratory indicators showed an area under the curve of 0.796 (95% CI, 0.777 to 0.814), with a sensitivity of 46.93% and a specificity of 90.09% when using a cutoff value of 0.598. Conclusions Some routine laboratory results had statistical difference between NCPP and IP. A diagnostic model based on combination of routine laboratory results provides an adjunct approach in the differential diagnosis between NCPP and IP. url: https://www.sciencedirect.com/science/article/pii/S1201971220302952?v=s5 doi: 10.1016/j.ijid.2020.04.078 id: cord-304872-hnxmtbrf author: Lv, Hao title: Prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with COVID‑19 in Wuhan, China date: 2020-09-17 words: 3433.0 sentences: 204.0 pages: flesch: 56.0 cache: ./cache/cord-304872-hnxmtbrf.txt txt: ./txt/cord-304872-hnxmtbrf.txt summary: OBJECTIVES: To investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (COVID-19) in Wuhan using a telephone interview. The characteristics of the patient''s disease course and recovery time for olfactory and/or gustatory dysfunctions (OD and/or GD) were collected by telephone interview. Two hypotheses might explain the low prevalence of OD and/ or GD reported in the Chinese study: First, the number of Chinese patients with COVID-19 who exhibit olfactory or gustatory disorders is indeed lower. Furthermore, all previous studies were limited to the acute phase with a short follow-up period, which might not reflect the recovery regularity of olfactory and/or gustatory impairment in patients with COVID 19. The aim of this study was to investigate the occurrence and recovery time of olfactory and/or gustatory dysfunction in patients with COVID-19 infection who were discharged from non-intensive care units 3 months earlier in China. abstract: OBJECTIVES: To investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (COVID-19) in Wuhan using a telephone interview. METHODS: This retrospective telephone survey investigated 196 consecutive patients with COVID-19 discharged 3 months previously from two hospital in Wuhan, China. The characteristics of the patient's disease course and recovery time for olfactory and/or gustatory dysfunctions (OD and/or GD) were collected by telephone interview. Demographic data were collected from the patients’ medical records. RESULTS: A total of 196 patients with COVID-19 completed the study. The most prevalent general symptoms consisted of fever, cough, and fatigue. 19.9% of patients reported OD and/or GD. In 87.2% of these cases, OD or GD appeared after the general symptoms. Among the patients, 51.4% had a recovery time of more than 4 weeks for OD and/or GD. Patients with COVID-19 and OD and/or GD had significantly higher rates of cardiovascular disease than patients without OD and/or GD (p = 0.002). CONCLUSION: Recovery from chemosensory dysfunction (OD and/or GD) was slow, with over half of the patients taking more than 4 weeks to recover. Cardiovascular disease might be related to the development of olfactory or taste disorders in patients with COVID-19. url: https://doi.org/10.1016/j.ijid.2020.09.039 doi: 10.1016/j.ijid.2020.09.039 id: cord-310691-6danlh8h author: Ma, Simin title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China date: 2020-05-26 words: 2297.0 sentences: 149.0 pages: flesch: 57.0 cache: ./cache/cord-310691-6danlh8h.txt txt: ./txt/cord-310691-6danlh8h.txt summary: title: Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China Our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill COVID-19 patients, leading to serious complications such as shock, ARDS, fulminant myocarditis, acute kidney injure or multiple organ failure (Cao 2020; Ruan et al. To the best of our knowledge, this is the first study of co-infection with SARS-CoV-2 and the influenza virus among critically ill COVID-19 patients. Co-infection with SARS-CoV-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill COVID-19 patients. The submission of manuscript entitled "Clinical Characteristics of Critically Ill Patients Co-infected with SARS-CoV-2 and the Influenza Virus in Wuhan, China" to "International Journal of Infectious Diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. abstract: OBJECTIVE: To delineate the clinical characteristics of critically ill COVID-19 patients co-infected with influenza. METHODS: In this study, we included adult patients with laboratory-confirmed COVID-19 form Tongji Hospital (Wuhan, China), with or without influenza, and compared their clinical characteristics. RESULTS: Among 93 patients, 44 died and 49 were discharged. Forty-four (47.3%) were infected with influenza virus A and 2 (2.2%) with influenza virus B. Twenty-two (50.0%) of the non-survivors and 24 (49.0%) of the survivors were infected with the influenza virus. Critically ill COVID-19 patients with influenza were more prone to cardiac injury than those without influenza. For the laboratory indicators at admission, white blood cell counts, neutrophil counts, levels of tumor necrosis factor-α, D-dimer value, and proportion of elevated creatinine were higher in non-survivors with influenza than in those without influenza. CONCLUSION: The results showed a high proportion of COVID-19 patients were co-infected with influenza in Tongji Hospital, with no significant difference in the proportion of co-infection between survivors and non-survivors. The critically ill COVID-19 patients with influenza exhibited more severe inflammation and organ injury, indicating that co-infection with the influenza virus may induce an earlier and more frequently occurring cytokine storm. url: https://www.ncbi.nlm.nih.gov/pubmed/32470606/ doi: 10.1016/j.ijid.2020.05.068 id: cord-278406-n5e3a09i author: Macauley, Precious title: CORTICOSTEROIDS IN THE TREATMENT OF SEVERE COVID-19 LUNG DISEASE: THE PULMONOLOGY PERSPECTIVE FROM THE FIRST UNITED STATES EPICENTER date: 2020-08-21 words: 1492.0 sentences: 79.0 pages: flesch: 39.0 cache: ./cache/cord-278406-n5e3a09i.txt txt: ./txt/cord-278406-n5e3a09i.txt summary: Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (Massachusetts General Hospital, 2020), societal guidelines (Bhimarj et al, 2020), and position statements (Russell et al, 2020) . All too frequently, the features of lung involvement in severe COVID-19 have been conflated with the acute respiratory distress syndrome (ARDS), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (DAD). abstract: The SARS-CoV-2 pandemic has introduced the medical community to a lung disease heretofore unknown to most clinicians. In much of the discourse about COVID-19 lung disease, the more familiar clinical entity of ARDS has been used as the guiding paradigm. Reflecting on studies in ARDS, particularly that due to influenza, and on data from the SARS-CoV and MERS epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in COVID-19. The voice of the pulmonology community—the community of lung experts—has continued to be among the quietest in this conversation. Herein we offer our perspective as academic pulmonologists who encountered COVID-19 in its first United States epicenter of New York City. We encourage a conceptual separation between early COVID-19 lung involvement and ARDS. We draw on history with other immune cell-mediated lung diseases, on insights from the SARS-CoV experience, and on frontline observations in an attempt to allay the skepticism towards corticosteroids in COVID-19 lung disease that is likely to persist even as favorable study results emerge. url: https://doi.org/10.1016/j.ijid.2020.08.051 doi: 10.1016/j.ijid.2020.08.051 id: cord-297715-qcwp2jdv author: Machida, Masaki title: Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak date: 2020-05-17 words: 2152.0 sentences: 111.0 pages: flesch: 48.0 cache: ./cache/cord-297715-qcwp2jdv.txt txt: ./txt/cord-297715-qcwp2jdv.txt summary: title: Changes in implementation of personal protective measures by ordinary Japanese citizens: A longitudinal study from the early phase to the community transmission phase of the COVID-19 outbreak Participants were asked how often they implemented the 5 personal protective measures recommended by the World Health Organization (hand hygiene, social distancing, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) in the baseline and follow-up surveys. In that study, we found that in the early phase of COVID-19 there was J o u r n a l P r e -p r o o f low prevalence among ordinary Japanese citizens in the implementation of social distancing measures and avoiding touching the eyes, nose and mouth, 2 of the 5 personal protective measures recommended by the World Health Organization (WHO) (WHO, 2020a The company, then invited the 2,400 respondents of the baseline survey to participate in a follow-up survey by email on April 1, 2020. abstract: OBJECTIVES: To clarify changes in the implementation of personal protective measures among ordinary Japanese citizens from the early phase of the COVID-19 outbreak to the community transmission phase. METHODS: This longitudinal, internet-based survey included 2,141 people (50.8% men; 20-79 years). The baseline and follow-up surveys were conducted from February 25-27, 2020 and April 1-6, 2020, respectively. Participants were asked how often they implemented the 5 personal protective measures recommended by the World Health Organization (hand hygiene, social distancing, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) in the baseline and follow-up surveys. RESULTS: The prevalence of 3 of the 5 personal protective measures significantly improved in the community transmission phase compared to the early phase. Social distancing measures showed significant improvement, from 67.4% to 82.2%. However, the prevalence of avoiding touching the eyes, nose and mouth, which had the lowest prevalence in the early phase, showed no significant improvement (approximately 60%). Multivariate logistic regression analysis revealed, men and persons of low-income households made fewer improvements than women and persons of high-income households. CONCLUSIONS: The prevalence of personal protective measures by ordinary citizens is improving, however there is potential for improvement, especially in regard to avoiding touching eyes, nose and mouth. url: https://doi.org/10.1016/j.ijid.2020.05.039 doi: 10.1016/j.ijid.2020.05.039 id: cord-029882-kufs0fxe author: Malviya, Amit title: The continued dilemma about usage of Hydroxychloroquine: Respite is in randomized control trials date: 2020-07-29 words: 483.0 sentences: 34.0 pages: flesch: 57.0 cache: ./cache/cord-029882-kufs0fxe.txt txt: ./txt/cord-029882-kufs0fxe.txt summary: HCQ is touted for treatment of Covid 19 primarily based on its anti-viral properties, thus the timing of administration becomes very important for a meaning full assessment of study results. Recently it been shown that this score is not accurate for predicting severity of disease in Covid 19 patients . Covid 19 is a multisystem disease and the disease itself promotes proarrhythmic milieu with prolonged QT intervals at baseline .5,6 Risk assessment of HCQ therapy is not complete if such patients are excluded. Finally , mechanism of action of HCQ against is a part of its broad anti-viral and immunomodulatory properties and no specific pharmacologic actions are described for SARS-CoV-2 infection. 9,10 Weather HCQ as initial anti-viral agent prevents progression to severe disease is not known clearly . Ventricular arrhythmia risk due to chloroquine / hydroxychloroquine treatment for COVID-19: Should it be given Effects of chloroquine on viral infections: an old drug against today''s diseases? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388893/ doi: 10.1016/j.ijid.2020.07.054 id: cord-318315-r6wqywwe author: Memish, Ziad A. title: Etiology of severe community-acquired pneumonia during the 2013 Hajj—part of the MERS-CoV surveillance program date: 2014-06-23 words: 3090.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-318315-r6wqywwe.txt txt: ./txt/cord-318315-r6wqywwe.txt summary: We aimed to screen Hajj pilgrims admitted to healthcare facilities in 2013 with severe community-acquired pneumonia (CAP) for MERS-CoV and to determine other etiologies. METHODS: Sputum samples were collected from all pilgrims admitted to 15 healthcare facilities in the cities of Makkah and Medina, Saudi Arabia, who were diagnosed with severe CAP on admission, presenting with bilateral pneumonia. 7, 10 In recent years, the Middle East respiratory syndrome coronavirus (MERS-CoV) has also emerged as a cause of serious illness including severe pneumonia. Respiratory tract infections are common illnesses during the Hajj, 15 and pneumonia is the leading cause of hospital admission, including admission to the ICU, during the pilgrimage. 16 In the current study, as part of the Saudi MoH MERS-CoV surveillance, we investigated the etiology of severe CAP in pilgrims attending the 2013 Hajj requiring hospitalization. 7,10 Studies performed during previous Hajj seasons have reported the organism as a cause of respiratory tract infections including penumonia. abstract: BACKGROUND: Pneumonia is the leading cause of hospital admission during the annual Islamic pilgrimage (Hajj). The etiology of severe pneumonia is complex and includes the newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV). Since 2012, the Saudi Ministry of Health (MoH) has required screening for MERS-CoV for all cases of severe pneumonia requiring hospitalization. We aimed to screen Hajj pilgrims admitted to healthcare facilities in 2013 with severe community-acquired pneumonia (CAP) for MERS-CoV and to determine other etiologies. METHODS: Sputum samples were collected from all pilgrims admitted to 15 healthcare facilities in the cities of Makkah and Medina, Saudi Arabia, who were diagnosed with severe CAP on admission, presenting with bilateral pneumonia. The medical records were reviewed to collect information on age, gender, nationality, and patient outcome. Samples were screened for MERS-CoV by PCR, and a respiratory multiplex array was used to detect up to 22 other viral and bacterial respiratory pathogens. RESULTS: Thirty-eight patients met the inclusion criteria; they were predominantly elderly (mean age 58.6 years, range 25–83 years) and male (68.4%), and all were from developing countries. Fourteen of the 38 patients died (36.8%). MERS-CoV was not detected in any of the samples. Other respiratory pathogens were detected in 26 (68.4%) samples. Of these, bacterial pathogens were detected in 84.6% (22/26) and viruses in 80.7% (21/26). Twenty-one (80.7%) samples were positive for more than one respiratory pathogen and 17 (65.3%) were positive for both bacteria and viruses. The most common respiratory virus was human rhinovirus, detected in 57.7% of the positive samples, followed by influenza A virus (23.1%) and human coronaviruses (19.2%). Haemophilus influenzae and Streptococcus pneumoniae were the predominant bacteria, detected in 57.7% and 53.8%, respectively, of the positive samples, followed by Moraxella catarrhalis (36.4%). CONCLUSIONS: MERS-CoV was not the cause of severe CAP in any of the hospitalized pilgrims investigated. However we identified a variety of other respiratory pathogens in the sputum of this small number of patients. This indicates that the etiology of severe CAP in Hajj is complex with implications regarding its management. url: https://www.ncbi.nlm.nih.gov/pubmed/24970703/ doi: 10.1016/j.ijid.2014.06.003 id: cord-292256-jp80u828 author: Moriguchi, Takeshi title: A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 date: 2020-04-03 words: 1742.0 sentences: 121.0 pages: flesch: 53.0 cache: ./cache/cord-292256-jp80u828.txt txt: ./txt/cord-292256-jp80u828.txt summary: We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. (Wang et al., 2020a,b) A preliminary report warned that SARS-CoV-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . This brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with SARS-CoV-2 RNA in cerebrospinal fluid. This case shows the neuroinvasive potential of the virus and that we cannot exclude SARS-CoV-2 infections even if the RT-PCR test for SARS-CoV-2 using the patient''s nasopharyngeal specimen is negative. abstract: Novel coronavirus (SARS-Coronavirus-2:SARS-CoV-2) which emerged in Wuhan, China, has spread to multiple countries rapidly. We report the first case of meningitis associated with SARS-CoV-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. He had never been to any foreign countries. He felt generalized fatigue and fever (day 1). He saw doctors nearby twice (day 2 and 5) and was prescribed Laninamivir and antipyretic agents, His family visited his home and found that he was unconsciousness and lying on the floor in his vomit. He was immediately transported to this hospital by ambulance (day 9). Under emergency transport, he had transient generalized seizures that lasted about a minute. He had obvious neck stiffness. The specific SARS-CoV-2 RNA was not detected in the nasopharyngeal swab but was detected in a CSF. Anti- HSV 1 and varicella-zoster IgM antibodies were not detected in serum samples. A brain MRI showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of SARS-CoV-2 meningitis. This case warns the physicians of patients who have CNS symptoms. url: https://doi.org/10.1016/j.ijid.2020.03.062 doi: 10.1016/j.ijid.2020.03.062 id: cord-315059-l6guql8q author: Mubarak, Naeem title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. Time for some unpopular decisions date: 2020-04-30 words: 475.0 sentences: 44.0 pages: flesch: 73.0 cache: ./cache/cord-315059-l6guql8q.txt txt: ./txt/cord-315059-l6guql8q.txt summary: title: Corona and Clergy: The missing link for an effective social distancing in Pakistan. To begin with, more than half of the COVID-19 cases in Malaysia received virus 11 in a congregation of 16000 believers from 30 countries. Pakistan''s case is of concern due to a fragile healthcare system, poor hygiene practices, 20 limited access to healthcare, and steep rise in the number of local cases in a population bigger 21 than Italy and Iran combined. Evidence supports the substantial impact of social distancing as 22 a viable practice to contain the spread of the virus. In Pakistan, the practice of social distancing 24 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 Muslim world, and cancelled Umrah (pilgrimage). for Pakistan to implement social distancing in the holy month of Ramadan (26 th April) when 46 influx in mosques increases many-fold for daily prayers and Tarawih (an additional prayer in 47 Email: naeem.mubarak@lmdc.edu.pk Tel: 00-92-42-37392215 79 80 COVID-19: Pakistan to allow mosques prayers in 70 abstract: nan url: https://doi.org/10.1016/j.ijid.2020.04.067 doi: 10.1016/j.ijid.2020.04.067 id: cord-273961-ja8xggnd author: Nakagawara, Kensuke title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections date: 2020-07-26 words: 784.0 sentences: 54.0 pages: flesch: 58.0 cache: ./cache/cord-273961-ja8xggnd.txt txt: ./txt/cord-273961-ja8xggnd.txt summary: title: Acute Onset Olfactory/Taste Disorders are Associated with a High Viral Burden in Mild or Asymptomatic SARS-CoV-2 Infections We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. Real-time polymerase chain reaction (qPCR) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qPCR cycle threshold (Ct) values and disease severity (1, 2) . Specifically, Ct values from qPCR tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using Ct values (1, 2) . abstract: We investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild SARS-CoV-2 infection using cycle threshold (Ct) qPCR values. Patients with olfactory/taste disorders (OTDs) exhibited lower qPCR Ct values and longer time to negative qPCR than those without OTDs, suggesting association between OTDs and high viral burden. url: https://doi.org/10.1016/j.ijid.2020.07.034 doi: 10.1016/j.ijid.2020.07.034 id: cord-297396-r1p7xn3a author: Ng, Ming-Yen title: Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date: 2020-09-15 words: 3251.0 sentences: 182.0 pages: flesch: 53.0 cache: ./cache/cord-297396-r1p7xn3a.txt txt: ./txt/cord-297396-r1p7xn3a.txt summary: OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.  Developed two simple-to use nomograms for identifying COVID-19 positive patients  Probabilities are provided to allow healthcare leaders to decide suitable cut-offs  Variables are age, white cell count, chest x-ray appearances and contact history  Model variables are easily available in the general hospital setting. To develop: (1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. Thus, a COVID-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such RT-PCR availability is constrained. abstract: OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. METHODS: Patients with and without COVID-19 were included from 4 Hong Kong hospitals. Database was randomly split 2:1 for model development database (n = 895) and validation database (n = 435). Multivariable logistic regression was utilised for model creation and validated with the Hosmer-Lemeshow (H-L) test and calibration plot. Nomograms and probabilities set at 0.1, 0.2, 0.4, 0.6 were calculated to determine sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). RESULTS: 1330 patients (mean age 58.2 ± 24.5 years; 50.7% males; 296 COVID-19 positive) were recruited. First prediction model developed had age, total white blood cell count, chest x-ray appearances and contact history as significant predictors (AUC = 0.911 [CI = 0.880-0.941]). Second model developed has same variables except contact history (AUC = 0.880 [CI = 0.844-0.916]). Both were externally validated on H-L test (p = 0.781 and 0.155 respectively) and calibration plot. Models were converted to nomograms. Lower probabilities give higher sensitivity and NPV; higher probabilities give higher specificity and PPV. CONCLUSION: Two simple-to-use validated nomograms were developed with excellent AUCs based on readily available parameters and can be considered for clinical utilisation. url: https://api.elsevier.com/content/article/pii/S1201971220307384 doi: 10.1016/j.ijid.2020.09.022 id: cord-340992-88t1c0zs author: Nikolai, Lea A title: Asymptomatic SARS Coronavirus 2 infection: Invisible yet invincible date: 2020-09-03 words: 3092.0 sentences: 193.0 pages: flesch: 44.0 cache: ./cache/cord-340992-88t1c0zs.txt txt: ./txt/cord-340992-88t1c0zs.txt summary: Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The first study cluster comprised of five family members from Anyang, China, who developed COVID-19 symptoms and tested positive by RT-PCR after acquiring the infection from the index case, an asymptomatic visitor from Wuhan who later tested positive 20 . Similar to the Diamond Princess, another study of an Argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for COVID-19; 81% of those infected were asymptomatic virus carriers 24 . When assessing public health risks raised by asymptomatic COVID-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. Since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of COVID-19. Asymptomatic cases in a family cluster with SARS-CoV-2 infection abstract: While successful containment measures of COVID-19 in China and many European countries have led to flattened curves, case numbers are rising dramatically in other countries, with the emergence of a second wave expected. Asymptomatic individuals carrying SARS-CoV-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. The data addressed here show that characteristics of asymptomatic and presymptomatic infection are not identical. Younger age correlates strongly with asymptomatic and mild infections, and children as hidden drivers. The estimated proportion of asymptomatic infections ranges from 18% to 81%. The current perception of asymptomatic infections does not provide clear guidance for public-health measures. Asymptomatic infections will be a key contributor in COVID-19 spread. Asymptomatic cases should be reported in official COVID-19 statistics. url: https://www.sciencedirect.com/science/article/pii/S1201971220307062?v=s5 doi: 10.1016/j.ijid.2020.08.076 id: cord-356074-kw8c2fgk author: Oboh, Mary Aigbiremo title: Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks date: 2020-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Deadly emerging infectious pathogens place unprecedented challenge on health systems and economies, especially across Africa where health care infrastructures are weak, and poverty rates remain high. Genomic technologies have been vital in enhancing the understanding and development of intervention approaches against these, such as Ebola, and recently the novel coronavirus disease 2019 (COVID-19). DISCUSSION: Africa has contributed a limited number of SARS-CoV-2 genomes to the global pool in growing open access repositories. To bridge this gap, the Africa Centre for Disease Control and Prevention (ACDC) is coordinating initiatives across the continent to establish genomic hubs in selected well-resourced African centres of excellence. This will allow for standardisation, efficient and rapid data generation and curation. However, the strategy to ensure capacity for high-throughput genomics at selected genomics hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries. This will enhance small scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches at central genomic hubs. CONCLUSION: The ACDC needs to scale-up its campaign for government support across African Union countries to ensure sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in Africa. url: https://www.ncbi.nlm.nih.gov/pubmed/32800861/ doi: 10.1016/j.ijid.2020.08.027 id: cord-268599-z54p3dk3 author: Panda, Swagatika title: Human metapneumovirus: review of an important respiratory pathogen date: 2014-05-17 words: 5570.0 sentences: 308.0 pages: flesch: 39.0 cache: ./cache/cord-268599-z54p3dk3.txt txt: ./txt/cord-268599-z54p3dk3.txt summary: Human metapneumovirus (hMPV), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immune-compromised patients. Human metapneumovirus (hMPV), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immunecompromised patients. hMPV is the major etiological agent responsible for about 5% to 10% of hospitalizations of children suffering from acute respiratory tract infections. hMPV infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. hMPV infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. Detection of human metapneumovirus in hospitalized children with acute respiratory tract infection using real-time RT-PCR in a hospital in northern Taiwan Human metapneumovirus infection in young children hospitalized with respiratory tract disease abstract: Human metapneumovirus (hMPV), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immune-compromised patients. hMPV is the major etiological agent responsible for about 5% to 10% of hospitalizations of children suffering from acute respiratory tract infections. hMPV infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. Initial infection with hMPV usually occurs during early childhood, but re-infections are common throughout life. Due to the slow growth of the virus in cell culture, molecular methods (such as reverse transcriptase PCR (RT-PCR)) are the preferred diagnostic modality for detecting hMPV. A few vaccine candidates have been shown to be effective in preventing clinical disease, but none are yet commercially available. Our understanding of hMPV has undergone major changes in recent years and in this article we will review the currently available information on the molecular biology and epidemiology of hMPV. We will also review the current therapeutic interventions and strategies being used to control hMPV infection, with an emphasis on possible approaches that could be used to develop an effective vaccine against hMPV. url: https://doi.org/10.1016/j.ijid.2014.03.1394 doi: 10.1016/j.ijid.2014.03.1394 id: cord-288167-976qxja2 author: Park, Wan Beom title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date: 2018-05-09 words: 1373.0 sentences: 87.0 pages: flesch: 52.0 cache: ./cache/cord-288167-976qxja2.txt txt: ./txt/cord-288167-976qxja2.txt summary: title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. In the present study, replicative MERS-CoV was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in MERS-CoV-infected patients with severe pneumonia. In conclusion, replicative MERS-CoV was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic RNA. In upper respiratory tract specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. Middle East respiratory syndrome coronavirus (MERS-CoV) genomic RNA (upE) titers in sputum and transtracheal aspirates with vs. abstract: BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. The detection of MERS-CoV sub-genomic mRNAs indicates that the virus is replicative. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. METHODS: Upper and lower respiratory samples were obtained from 17 MERS-CoV-infected patients. MERS-CoV sub-genomic mRNA was detected by reverse transcription PCR (RT-PCR) and MERS-CoV genomic RNA by real-time RT-PCR. RESULTS: In sputum and transtracheal aspirate, sub-genomic mRNA was detected for up to 4 weeks after symptoms developed, which correlated with the detection of genomic RNA. In oropharyngeal and nasopharyngeal swab specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. CONCLUSIONS: These findings suggest that MERS-CoV does not replicate well in the upper respiratory tract. url: https://api.elsevier.com/content/article/pii/S1201971218344114 doi: 10.1016/j.ijid.2018.05.003 id: cord-276254-q04hqra2 author: Paul, Kishor Kumar title: Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh date: 2020-06-02 words: 3829.0 sentences: 202.0 pages: flesch: 50.0 cache: ./cache/cord-276254-q04hqra2.txt txt: ./txt/cord-276254-q04hqra2.txt summary: title: Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh In this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. (Khatun et al., 2015 , Salje et al., 2016b Here we use the results from a detailed investigation of an outbreak of chikungunya virus in a village in Tangail, Bangladesh where the outbreak team visited every household in the community and interviewed all members in each household. This investigation suggests that chikungunya virus has become an emerging public health problem in Bangladesh, and outbreak investigations of emerging infections often have the objective of estimating attack rates of diseases and identifying the risk factors that lead to infection. abstract: Abstract Background Outbreak investigations typically focus their efforts on identifying cases that present at healthcare facilities. However, these cases rarely represent all cases in the wider community. In this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. Methods We used different subsets of the data from a comprehensive outbreak investigation to compare the inferences we make in alternative investigation strategies. Results The outbreak investigation team interviewed 1,933 individuals from 460 homes. 364 (18%) of individuals had symptoms consistent with chikungunya. A theoretical clinic-based study would have identified 26% of the cases. Adding in community-based cases provided an overall estimate of the attack rate in the community. Comparison with controls from the same household revealed that those with at least secondary education had a reduced risk. Finally, enrolling residents from households across the community allowed us to characterize spatial heterogeneity of risk and identify the type of clothing usually worn and travel history as risk factors. This also revealed that household-level use of mosquito control was not associated with infection. Conclusions These findings highlight that while clinic-based studies may be easier to conduct, they only provide limited insight into the burden and risk factors for disease. Enrolling people who escaped from infection, both in the household and in the community allows a step change in our understanding of the spread of a pathogen and maximizes opportunities for control. url: https://doi.org/10.1016/j.ijid.2020.05.111 doi: 10.1016/j.ijid.2020.05.111 id: cord-306200-d5qn65k0 author: Petersen, Eskild title: COVID-19 travel restrictions and the International Health Regulations – call for an open debate on easing of travel restrictions date: 2020-04-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220302459?v=s5 doi: 10.1016/j.ijid.2020.04.029 id: cord-311026-mpr3xb2a author: Petersen, Eskild title: COVID-19–We urgently need to start developing an exit strategy date: 2020-04-29 words: 5624.0 sentences: 339.0 pages: flesch: 56.0 cache: ./cache/cord-311026-mpr3xb2a.txt txt: ./txt/cord-311026-mpr3xb2a.txt summary: Another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. Thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in Taiwan, Korea and Oman, summarized in table 3. Despite the city state''s strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (SCMP 3 rd April). This initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. abstract: Abstract Aim The purpose of this perspective is to review the options countries have to exit the draconian “lock downs” in a carefully staged manner. Methods Experts from different countries experiencing Corona Virus Infectious Disease 2019 (COVID-19) review evidence and country specific approaches and results of their interventions. Results Three key factors are important: 1. Reintroduction from countries with ongoing community transmission; 2. The need for extensive testing capacity and widespread community testing, and 3. Adequate supply of personal protective equipment, PPE, to protect health care workers. Lifting social distancing is discussed at length. How to open manufacturing, construction and logistics. The opening og higher educational institutions and schools. The use of electronic surveillance is discussed. Conclusion Each country has to decide what is the best path forward. However, we can learn from each other and the approach is in reality very similar. url: https://www.ncbi.nlm.nih.gov/pubmed/32360552/ doi: 10.1016/j.ijid.2020.04.035 id: cord-317080-kn56oov6 author: Quadri, Sayed. A. title: COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens date: 2020-05-07 words: 289.0 sentences: 31.0 pages: flesch: 59.0 cache: ./cache/cord-317080-kn56oov6.txt txt: ./txt/cord-317080-kn56oov6.txt summary: title: COVID-19 and Religious Congregations: Implications for Spread of Novel Pathogens Gathering of large number of people in close approximation could be a fertile ground for the spread of novel pathogens. COVID 19 is spread through droplet and basic reproduction rate, a 23 measure of transmissibility of the virus, ranges from 2.24 to 3.58 (Zhao et al., 2020) . Public 24 gatherings will evidently increase transmission and therefore social distancing was touted as the 25 foremost preventive strategy.  Suspension of communal gatherings must be promptly done as a preventive strategy 196 whenever novel pathogens emerge, in order to contain its spread.  An international regime of containment measures with regards to suspension of religious 198 congregations during infectious disease outbreaks must be devised. Preliminary estimation of the basic reproduction number of novel 185 coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the 186 early phase of the outbreak abstract: Abstract COVID-19 pandemic is ravaging the world. One of the principle preventive strategies is practicing social distancing. Congregations of the faithful at local and transnational level are strongly recommended by several world religions and religious orders. Gathering of large number of people in close approximation could be a fertile ground for the spread of novel pathogens. The refusal to suspend such gatherings could lead to potential widespread dispersal of infections. url: https://www.sciencedirect.com/science/article/pii/S1201971220303131?v=s5 doi: 10.1016/j.ijid.2020.05.007 id: cord-338576-gh1plurq author: Regen, Francesca title: A Simple Approach to Optimum Pool Size for Pooled SARS-CoV-2 Testing date: 2020-08-28 words: 1201.0 sentences: 69.0 pages: flesch: 54.0 cache: ./cache/cord-338576-gh1plurq.txt txt: ./txt/cord-338576-gh1plurq.txt summary: Finally, we derive a simple-to-use formula and table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. Here we provide a simple strategy to estimate the optimum pool size for a two-staged pooling based on a known target prevalence. The optimum pool size for a given frequency is defined by the local minima of the isolines in figure 1A and can be more precisely determined by the first derivative of equation 1 Results from our analysis clearly demonstrate the relation between target prevalence rates and optimum pool sizes in a two staged pooling strategy. The relation between the estimated analyses per specimen and a pool size are given for various target prevalence rates as defined by equation 1 (isolines; A). Local minima suggest optimum pool sizes at the respective target prevalence rate (isolines; A). abstract: Systematic, large-scale testing of asymptomatic subjects is an important strategy in the management of the SARS-CoV-2 pandemic. In order to increase the capacity of laboratory-based molecular SARS-CoV-2 testing, it has been suggested to combine several samples and jointly measure them in a sample pool. While saving cost and labour at first sight, pooling efficiency depends on the pool size and the presently experienced prevalence of positive samples. Here we address the question of the optimum pool size at a given prevalence. We demonstrate the relation between analytical effort and pool size and delineate the effects of the target prevalence on the optimum pool size. Finally, we derive a simple-to-use formula and table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. url: https://www.ncbi.nlm.nih.gov/pubmed/32866638/ doi: 10.1016/j.ijid.2020.08.063 id: cord-280060-gzby85u9 author: Rello, Jordi title: Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() date: 2016-04-28 words: 5493.0 sentences: 297.0 pages: flesch: 38.0 cache: ./cache/cord-280060-gzby85u9.txt txt: ./txt/cord-280060-gzby85u9.txt summary: 2 A International Journal of Infectious Diseases 48 (2016) 104-112 significant number of immunocompromised patients may also be migrants who may return to their countries of origin to visit friends and relatives, and may acquire travel-associated infections. 26 Cases of Chagas disease (Trypanosoma cruzi) either as a consequence of reactivation of a latent infection not identified at the time of transplant (because an unrecorded travel history or stay in an endemic area) or by transmission through the organ donor, can also be associated with a high mortality. There have also been case reports of severe disease from other travel-associated infections, such as salmonellosis, Vibrio parahaemolyticus, and visceral leishmaniasis in immunocompromised patients. Less common pathogens such as Staphylococcus aureus, avian influenza viruses such as H7N9 and H5N1, the Middle East respiratory syndrome coronavirus (MERS-CoV), and Gram-negative rods such as Burkholderia pseudomallei must also be considered, as well as a few other pathogens that do not usually cause pneumonia, such as malaria. abstract: This position paper is the second ESCMID Consensus Document on this subject and aims to provide intensivists, infectious disease specialists, and emergency physicians with a standardized approach to the management of serious travel-related infections in the intensive care unit (ICU) or the emergency department. This document is a cooperative effort between members of two European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study groups and was coordinated by Hakan Leblebicioglu and Jordi Rello for ESGITM (ESCMID Study Group for Infections in Travellers and Migrants) and ESGCIP (ESCMID Study Group for Infections in Critically Ill Patients), respectively. A relevant expert on the subject of each section prepared the first draft which was then edited and approved by additional members from both ESCMID study groups. This article summarizes considerations regarding clinical syndromes requiring ICU admission in travellers, covering immunocompromised patients. url: https://doi.org/10.1016/j.ijid.2016.04.020 doi: 10.1016/j.ijid.2016.04.020 id: cord-344478-5gp7v1uh author: Rosenberg, Eli S. title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 date: 2020-07-29 words: 760.0 sentences: 56.0 pages: flesch: 53.0 cache: ./cache/cord-344478-5gp7v1uh.txt txt: ./txt/cord-344478-5gp7v1uh.txt summary: title: Clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with COVID-19 The study from Arshad et al on the use of hydroxychloroquine, with and without azithromycin, for the treatment of inpatients with COVID-19 in one healthcare system (Henry Ford Health System) is a new entrant into the rapidly expanding literature on the treatment of this disease [1, 2] . Treatment with Hydroxychloroquine, Azithromycin, and Combination in Patients Hospitalized with COVID-19 Observational Study of Hydroxychloroquine in Hospitalized Patients with Covid-19 Association of Treatment With Hydroxychloroquine or Azithromycin With In-Hospital Mortality in Patients With COVID-19 in Treatment with Hydroxychloroquine Cut Death Rate Significantly in COVID-19 Patients, Henry Ford Health System Study Shows abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32738483/ doi: 10.1016/j.ijid.2020.07.055 id: cord-253102-z15j8izi author: Ross, Allen G.P. title: Planning for the Next Global Pandemic date: 2015-08-04 words: 2907.0 sentences: 171.0 pages: flesch: 54.0 cache: ./cache/cord-253102-z15j8izi.txt txt: ./txt/cord-253102-z15j8izi.txt summary: The West African Ebola virus pandemic has shown us yet again that the world is ill prepared to respond to a global health emergency. The national health systems in West Africa, and for most low and middle income countries (LMICs), would not meet IHR standards (despite claims by some member WHA nations) and it is unlikely that following the Ebola pandemic much will change. This editorial discusses many issues including priority emerging and reemerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the One Health approach to future pandemic planning. The PEF would 22 If the WHO contingency fund (100 million US dollars) and the World Bank pandemic emergency facility cannot be utilised to strengthen national health systems in LMICs in order to meet IHRs core capabilities, then how can this be achieved? abstract: In order to mitigate human and financial losses as a result of future global pandemics, we must plan now. As the Ebola virus pandemic declines, we must reflect on how we have mismanaged this recent international crisis and how we can better prepare for the next global pandemic. Of great concern is the increasing frequency of pandemics occurring over the last few decades. Clearly, the window of opportunity to act is closing. This editorial discusses many issues including priority emerging and re-emerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the One Health approach to future pandemic planning. We recommend that the global health community unites to urgently address these issues in order to avoid the next humanitarian crisis. url: https://api.elsevier.com/content/article/pii/S1201971215001836 doi: 10.1016/j.ijid.2015.07.016 id: cord-316209-juvmabdq author: Rutayisire, Erigene title: What works and what does not work in response to COVID-19 prevention and control in Africa date: 2020-06-12 words: 2335.0 sentences: 112.0 pages: flesch: 54.0 cache: ./cache/cord-316209-juvmabdq.txt txt: ./txt/cord-316209-juvmabdq.txt summary: The lower number of COVID-19 cases in most African countries is attributed to inadequate health systems, low-to-absent testing capacity, poor reporting system and insufficient number of medical staff. On 11 March 2020, the World Health Organization (WHO) had declared COVID-19 a pandemic, pointing to the over 118,000 cases of the coronavirus illnesses in over 110 countries and territories around the world and the sustained risk of further global spread. Africa Centers for Diseases Control and Prevention (Africa CDC), World Health Organization and other international agencies are providing support and guidance to many African countries in response to COVID-19 pandemic. Despite reported low case-fatality of COVID-19, the pandemic is likely to cause more deaths in Africa if the compliance to COVID-19 prevention and control measures continues to be ignored as observed in some African countries. abstract: Abstract Since the emergence of the pandemic in December 2019 in Wuhan, China, as of 10:00 CEST, June 6, 2020, there have been nearly 6,663,304 confirmed cases of COVID-19 including 392,802 deaths worldwide. In Africa, as of June 2, 2020, a total of 152,442 COVID-19 cases and 4334 deaths have been reported. The five countries with the highest commutative number of cases in Africa are South Africa, Egypt, Nigeria, Algeria, and Ghana. Africa, together with the rest of world have had to swiftly undertake measures necessary to protect the continent from irreversible effects of the COVID-19 pandemic that is claiming lives and destroying livelihoods. The lower number of COVID-19 cases in most African countries is attributed to inadequate health systems, low-to-absent testing capacity, poor reporting system and insufficient number of medical staff. The COVID-19 pandemic poses a great threat to most African countries from cities to rural areas and has created a strong demand on already scarce resources and requires an intense mobilization of additional resources to implement established emergency contingency measures. Closure of borders and movements of people restrictions within the country as measures to prevent the spread of COVID-19; this has resulted in the sector being adversely affected by the loss of income. Cooperative prevention and control measures are one of the promising solutions to deplete the spread of COVID-19 on the continent. url: https://api.elsevier.com/content/article/pii/S1201971220304604 doi: 10.1016/j.ijid.2020.06.024 id: cord-305782-gnzwe2z2 author: Satici, Celal title: Performance of Pneumonia Severity Index and CURB-65 in Predicting 30-day mortality in patients with COVID-19 date: 2020-06-14 words: 3363.0 sentences: 188.0 pages: flesch: 55.0 cache: ./cache/cord-305782-gnzwe2z2.txt txt: ./txt/cord-305782-gnzwe2z2.txt summary: Abstract Objective The aim of the study was to analyze the usefulness of the CURB-65 and pneumonia severity index (PSI) in predicting 30-day mortality in patients with COVID-19 and to identify other factors associated with higher mortality. Conclusion In a large group of hospitalized patients with COVID-19, we found that PSI performed better than CURB-65 in predicting mortality. According to the Health Ministry Guideline, any suspected case who is over 50 years old or has any comorbidity should be hospitalized irrespective of vital signs, laboratory results and computed tomography (CT) findings (Bilim Kurulu, 2020) Thus, a large proportion of patients with COVID-19 meet criteria for admission as an inpatient. In this study, we aimed to assess whether CURB-65 or PSI is useful tool to predict 30-day mortality and to identify other factors that are associated with higher mortality in patients with COVID-19. abstract: Abstract Objective The aim of the study was to analyze the usefulness of the CURB-65 and pneumonia severity index (PSI) in predicting 30-day mortality in patients with COVID-19 and to identify other factors associated with higher mortality. Methods A retrospective study was performed at a pandemic hospital in Istanbul, Turkey and 681 laboratory-confirmed patients with COVID-19 were included. Data on characteristics, vital signs and laboratory parameters were recorded form electronic medical records. We used receiver operating characteristic analysis to quantify the discriminatory abilities of the prognostic scales. Univariate and multivariate logistic regression analyses were performed to identify other predictors of mortality. Results Higher CRP levels were associated with an increased risk for mortality (OR:1.015, 95% CI 1.008 to 1.021, p < 0.001). The PSI performed significantly better than the CURB-65 (AUC: 0.91, 95% CI 0.88-0.93 vs AUC:0.88, 95% CI:0.85-0.90; p = 0.01) and the addition of CRP levels to PSI did not improve the performance of PSI in predicting mortality (AUC: 0.91, 95% CI 0.88-0.93 vs AUC:0.92, 95% CI:0.89-0.94; p = 0.29). Conclusion In a large group of hospitalized patients with COVID-19, we found that PSI performed better than CURB-65 in predicting mortality. Adding CRP levels to PSI did not improve the 30-day mortality prediction. url: https://www.ncbi.nlm.nih.gov/pubmed/32553714/ doi: 10.1016/j.ijid.2020.06.038 id: cord-317500-ufo2qgj4 author: Scialpi, Michele title: Pulmonary thromboembolism in criticall ill COVID-19 patients date: 2020-04-24 words: 428.0 sentences: 37.0 pages: flesch: 48.0 cache: ./cache/cord-317500-ufo2qgj4.txt txt: ./txt/cord-317500-ufo2qgj4.txt summary: Dear Editor, the outbreak of novel Coronavirus disease 2019 in the city of Wuhan, Hubei province of China, has been declared a pandemic by the World Health Organization (WHO) on March 21 st , and has since then forced the scientific community to consider two fundamental aspects: first off, SARS-CoV-2 does not only cause pneumonia and second, the death of many critical ill patients is caused by multiple organ failure (involving the heart, liver, kidneys, blood and immune system). A novel coronavirus from patients with pneumonia in China Acute pulmonary embolism and COVID-19 pneumonia: a random association? COVID-19 Complicated by Acute Pulmonary Embolism Radiology: Cardiothoracic Imaging Findings of Acute Pulmonary Embolism in COVID-19 Patients Management strategy of novel coronavirus (COVID-19) pneumonia in the radiology department: a Chinese experience The Authors declare no conflicts of interest associated for the manuscript entiltled "Pulmonary thromboembolism in criticall ill COVID-19 patients abstract: nan url: https://doi.org/10.1016/j.ijid.2020.04.056 doi: 10.1016/j.ijid.2020.04.056 id: cord-346461-eqyte6ko author: Scialpi, Michele title: Pneumonia misinterpretation in COVID-19: revisitation and update date: 2020-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220306962?v=s5 doi: 10.1016/j.ijid.2020.08.067 id: cord-341775-mucatzaa author: Shafi, Shuja title: The annual Hajj pilgrimage—minimizing the risk of ill health in pilgrims from Europe and opportunity for driving the best prevention and health promotion guidelines date: 2016-06-22 words: 2252.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-341775-mucatzaa.txt txt: ./txt/cord-341775-mucatzaa.txt summary: Mass gathering sporting and religious events pose important public health challenges, including the transmission of infectious diseases, exacerbation of non-communicable diseases, and disorders related to climate change. [1] [2] [3] [4] [5] Every year, the Kingdom of Saudi Arabia (KSA) hosts the Hajj pilgrimage, which is the largest mass gathering in the world held on a recurrent annual basis. Mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. abstract: Mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. Every year the Kingdom of Saudi Arabia (KSA) hosts the Hajj pilgrimage, the largest gathering held on an annual basis where over 2 million people come to KSA from over 180 countries. Living together in crowded conditions exposes the pilgrims and the local population to a range infectious diseases. Respiratory and gastrointestinal tract bacterial and viral infections can spread rapidly and affect attendees of mass gatherings. Lethal infectious disease outbreaks were common during Hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the KSA into public health prevention and surveillance programs. The KSA provides regular updated Hajj travel advice and health regulations through international public health agencies such as the WHO, Public Health England, the Centers for Disease Control and Prevention, and Hajj travel agencies. During the Hajj, an additional 25 000 health workers are deployed; there are eight hospitals in Makkah and Mina complete with state-of-the-art surgical wards and intensive care units made specifically available for pilgrims. All medical facilities offer high quality of care, and services are offered free to Hajj pilgrims to ensure the risks of ill health to all pilgrims and KSA residents are minimal. A summary of the key health issues that arise in pilgrims from Europe during Hajj and of the KSA Hajj guidelines, together with other factors that may play a role in reducing the risks to pilgrims and to wider global health security, is provided herein. url: https://doi.org/10.1016/j.ijid.2016.06.013 doi: 10.1016/j.ijid.2016.06.013 id: cord-284652-7npya3yx author: Shim, Eunha title: Spatial variability in reproduction number and doubling time across two waves of the COVID-19 pandemic in South Korea, February to July 2020 date: 2020-10-08 words: 3735.0 sentences: 172.0 pages: flesch: 55.0 cache: ./cache/cord-284652-7npya3yx.txt txt: ./txt/cord-284652-7npya3yx.txt summary: Results At the regional level, Seoul and Gyeonggi Province have experienced the first peak of COVID-19 in early March, followed by the second wave in early June, withRt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. Therefore, since 10 July, the government banned churches from organizing small gatherings other than regular worship services (KCDC, 2020a To estimate the regional and temporal variability in the reproduction number of COVID-19 in South Korea, including the second wave concentrated in the greater Seoul areas, we analysed the spatiotemporal progression of the epidemic in the country from mid-February to mid-July 2020. In this report, we estimated the doubling time and the effective reproduction number involving two epidemic waves of the COVID-19 epidemic in South Korea by employing the time series of cases by date of symptoms onset for the four most affected Korean regions: Seoul, Gyeonggi Province, Gyeongbuk Province, and Daegu. abstract: Objectives In South Korea, 13,745 cases of coronavirus disease (COVID-19) have been reported as of 19 July, 2020. To examine the spatiotemporal changes in the transmission potential, we present regional estimates of the doubling time and reproduction number (Rt ) of COVID-19 in the country. Methods Daily series of confirmed COVID-19 cases in the most affected regions were extracted from publicly available sources. We employed established mathematical and statistical methods to investigate the time-varying reproduction numbers of the COVID-19 in Korea and its doubling time, respectively. Results At the regional level, Seoul and Gyeonggi Province have experienced the first peak of COVID-19 in early March, followed by the second wave in early June, withRt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. As of 19 July, 2020, Gyeongbuk Province and Daegu are yet to experience a second wave of the disease, where the mean Rt reached 3.5-4.4 and doubling time ranging from 2.8 to 4.6 days during the first wave. Conclusions Our findings support the effectiveness of control measures against COVID-19 in Korea. However, the easing of the restrictions imposed by the government in May 2020 facilitated a second wave in the greater Seoul area. url: https://www.ncbi.nlm.nih.gov/pubmed/33038555/ doi: 10.1016/j.ijid.2020.10.007 id: cord-336954-rh88lod0 author: Shim, Eunha title: Transmission potential and severity of COVID-19 in South Korea date: 2020-03-18 words: 2972.0 sentences: 154.0 pages: flesch: 55.0 cache: ./cache/cord-336954-rh88lod0.txt txt: ./txt/cord-336954-rh88lod0.txt summary: OBJECTIVES: Since the first case of 2019 novel coronavirus (COVID-19) identified on Jan 20, 2020 in South Korea, the number of cases rapidly increased, resulting in 6,284 cases including 42 deaths as of March 6, 2020. However, the number of confirmed cases of SARS-CoV-2 infection started to increase rapidly on February 19, 2020 with a total of 6,284 confirmed COVID-19 cases including 42 deaths reported as of March 6, 2020 according to the Korea Centers for Disease Control and Prevention (KCDC) (KCDC, 2020) ( Table 1 ). Under the empirical reporting delay distribution from early Korean cases with available dates of onset, the intrinsic growth rate (r) was estimated at 0.6 (95% CI: 0.6, 0.7) and the scaling of growth parameter (p) was estimated at 0.8 (95% CI: 0.7, 0.8), indicating sub-exponential growth dynamics of COVID-19 abstract: OBJECTIVES: Since the first case of 2019 novel coronavirus (COVID-19) identified on Jan 20, 2020 in South Korea, the number of cases rapidly increased, resulting in 6,284 cases including 42 deaths as of March 6, 2020. To examine the growth rate of the outbreak, we aimed to present the first study to report the reproduction number of COVID-19 in South Korea. METHODS: The daily confirmed cases of COVID-19 in South Korea were extracted from publicly available sources. By using the empirical reporting delay distribution and simulating the generalized growth model, we estimated the effective reproduction number based on the discretized probability distribution of the generation interval. RESULTS: We identified four major clusters and estimated the reproduction number at 1.5 (95% CI: 1.4-1.6). In addition, the intrinsic growth rate was estimated at 0.6 (95% CI: 0.6, 0.7) and the scaling of growth parameter was estimated at 0.8 (95% CI: 0.7, 0.8), indicating sub-exponential growth dynamics of COVID-19. The crude case fatality rate is higher among males (1.1%) compared to females (0.4%) and increases with older age. CONCLUSIONS: Our results indicate early sustained transmission of COVID-19 in South Korea and support the implementation of social distancing measures to rapidly control the outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32198088/ doi: 10.1016/j.ijid.2020.03.031 id: cord-308080-1heu9vuv author: Simulundu, Edgar title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries date: 2020-10-06 words: 1714.0 sentences: 99.0 pages: flesch: 52.0 cache: ./cache/cord-308080-1heu9vuv.txt txt: ./txt/cord-308080-1heu9vuv.txt summary: title: First COVID-19 Case in Zambia – Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries Contact tracing showed that SARS-CoV-2 infection was contained within the patient''s household, with no further spread to attending health care workers or community members. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. We report the identification and clinical management of the first COVID-19 case from Zambia, and present the phylogenetic analyses of the patient''s SARS-CoV-2 isolate, comparing it to other SARS-CoV-2 lineages reported from other African countries. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1, sharing the most common recent ancestor with viruses detected in South Africa (Figure 2) Wuhan-Hu-1, which included the D614G mutation which has been observed to correlate with increased case fatality rates. abstract: Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. Whilst African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa.. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that lineage B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa. url: https://doi.org/10.1016/j.ijid.2020.09.1480 doi: 10.1016/j.ijid.2020.09.1480 id: cord-325325-xw7627x9 author: Skeik, Nedaa title: Influenza viruses and the evolution of avian influenza virus H5N1 date: 2007-10-02 words: 4079.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-325325-xw7627x9.txt txt: ./txt/cord-325325-xw7627x9.txt summary: While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. [8] [9] [10] [11] The 1957 pandemic was caused by the H2N2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. Although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. abstract: Although small in size and simple in structure, influenza viruses are sophisticated organisms with highly mutagenic genomes and wide antigenic diversity. They are species-specific organisms. Mutation and reassortment have resulted in newer viruses such as H5N1, with new resistance against anti-viral medications, and this might lead to the emergence of a fully transmissible strain, as occurred in the 1957 and 1968 pandemics. Influenza viruses are no longer just a cause of self-limited upper respiratory tract infections; the H5N1 avian influenza virus can cause severe human infection with a mortality rate exceeding 50%. The case death rate of H5N1 avian influenza infection is 20 times higher than that of the 1918 infection (50% versus 2.5%), which killed 675 000 people in the USA and almost 40 million people worldwide. While the clock is still ticking towards what seems to be inevitable pandemic influenza, on April 17, 2007 the U.S. Food and Drug Administration (FDA) approved the first vaccine against the avian influenza virus H5N1 for humans at high risk. However, more research is needed to develop a more effective and affordable vaccine that can be given at lower doses. url: https://www.sciencedirect.com/science/article/pii/S1201971207001531 doi: 10.1016/j.ijid.2007.07.002 id: cord-254872-w6d397js author: Stein, Richard A. title: Methicillin-resistant Staphylococcus aureus—the new zoonosis date: 2008-11-30 words: 1670.0 sentences: 90.0 pages: flesch: 36.0 cache: ./cache/cord-254872-w6d397js.txt txt: ./txt/cord-254872-w6d397js.txt summary: The surge in community-associated MRSA, at a time when reports of animal-to-human transmission are increasing, might not be merely coincidental, 12, 13 and according to a recent study conducted in the Netherlands, MRSA that entered from an animal reservoir into the human population is now responsible for over 20% of the strains isolated. 14 Findings that have accumulated in recent years make it necessary to define three additional patient groups at high risk for zoonotic MRSA: individuals in contact with farm animals, contacts of household pets, and veterinarian staff. Moreover, it is important to note that MRSA strains of animal origin have been isolated from people lacking previous documented direct animal contacts, supporting the possibility that direct human-to-human transmission occurs subsequent to one person''s colonization/infection. Methicillin (oxacillin)-resistant Staphylococcus aureus strains isolated from major food animals and their potential transmission to humans An outbreak of methicillin-resistant Staphylococcus aureus skin infections resulting from horse to human transmission in a veterinary hospital abstract: nan url: https://api.elsevier.com/content/article/pii/S1201971208015257 doi: 10.1016/j.ijid.2008.09.008 id: cord-279892-37vyazby author: Sun, Guanghao title: Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases date: 2017-01-16 words: 2904.0 sentences: 154.0 pages: flesch: 47.0 cache: ./cache/cord-279892-37vyazby.txt txt: ./txt/cord-279892-37vyazby.txt summary: This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. These systems have already been installed at most major international airports, and they can remotely sense several vital signs, including body temperature and heart and respiration rates, thereby facilitating the rapid and accurate screening of people who are suspected of carrying infectious diseases. To distinguish between patients with infectious influenza and healthy control subjects, logistic regression discriminant analysis was used to establish a classification model based on the three derived vital signs. The classification model was established using the data that described the three vital signs from the 16 influenza virus-infected patients and the 22 healthy control subjects using multivariable logistic regression. abstract: BACKGROUND: Infrared thermography (IRT) is used to screen febrile passengers at international airports, but it suffers from low sensitivity. This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. METHODS: An IRT system that produced visible and thermal images was used for image acquisition. The subjects’ respiration rates were measured by monitoring temperature changes around the nasal areas on thermal images; facial skin temperatures were measured simultaneously. Facial blood circulation causes tiny color changes in visible facial images that enable the determination of the heart rate. A logistic regression discriminant function predicted the likelihood of infection within 10 s, based on the measured vital signs. Sixteen patients with an influenza-like illness and 22 control subjects participated in a clinical test at a clinic in Fukushima, Japan. RESULTS: The vital-sign-based IRT screening system had a sensitivity of 87.5% and a negative predictive value of 91.7%; these values are higher than those of conventional fever-based screening approaches. CONCLUSIONS: Multiple vital-sign-based screening efficiently detected patients with suspected infectious diseases. It offers a promising alternative to conventional fever-based screening. url: https://api.elsevier.com/content/article/pii/S1201971217300103 doi: 10.1016/j.ijid.2017.01.007 id: cord-345275-h0hvaxgx author: Sun, Mengyao title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 words: 5308.0 sentences: 286.0 pages: flesch: 56.0 cache: ./cache/cord-345275-h0hvaxgx.txt txt: ./txt/cord-345275-h0hvaxgx.txt summary: title: Potential effective treatment for COVID-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy (iii) The intervention measure was convalescent blood products containing CP (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of CP therapy). A retrospective controlled study on SARS-CoV showed no deaths in 19 patients who received CP therapy, and there was a statistically significant difference in the case fatality ratio (CFR) compared with the control group (0% vs 23.8% 95% CI, 6 to 42 P=0.049) [10] . Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Retrospective study on collecting convalescent donor plasma for the treatment of patients with pandemic influenza A (H1N1) virus infection abstract: Abstract Background Convalescent plasma (CP) has been used successfully to treat many types of infectious diseases, and it has shown initial effects in the treatment of the emerging 2019 coronavirus disease (COVID-19). However, its curative effect and feasibility have yet to be confirmed by formal evaluation and well-designed clinical trials. To explore the effectiveness of treatment and predict the potential effect of CP for COVID-19, studies of different types of infectious diseases treated with CP were included in this systematic review and meta-analysis. Methods Related studies were obtained from databases and screened based on the inclusion criteria. The data quality was assessed, and the data were extracted and pooled for analysis. Results We included 40 studies on CP treatment for infectious diseases We found that CP treatment could reduce the risk of mortality with a low incidence of adverse events, promote the production of antibodies, show the decline in viral load, and shorten the disease course. A meta-analysis of 15 controlled studies showed that there was a significantly lower mortality rate in the group treated with CP (pooled OR = 0.32, 95% CI: 0.19-0.52, P < 0.001, I2 = 54%) than in the control groups. Studies were mostly of low or very low quality with a moderate or high risk of bias. The sources of clinical and methodological heterogeneity were identified. The exclusion of heterogeneity indicated that the results were stable. Conclusions CP therapy has some curative effect and is well tolerated to treat infectious diseases. It is a potentially effective treatment for COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1201971220305427?v=s5 doi: 10.1016/j.ijid.2020.06.107 id: cord-293942-n5ypkftc author: Takoi, Hiroyuki title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases date: 2020-09-28 words: 1160.0 sentences: 76.0 pages: flesch: 54.0 cache: ./cache/cord-293942-n5ypkftc.txt txt: ./txt/cord-293942-n5ypkftc.txt summary: title: Favipiravir-induced fever in coronavirus disease 2019: A report of two cases Favipiravir, an antiviral agent, is undergoing clinical trials for treating novel coronavirus disease 2019 (COVID-19). We report two cases of COVID-19 with favipiravir-induced fever. Favipiravir, a promising antiviral agent, is undergoing clinical trials as an alternative drug for treating COVID-19 (Arab-Zozani et al., 2020) in several countries, including China (Chen et al., 2020) , Iran, Germany, and Japan. We experienced two cases of favipiravir-induced fever in patients hospitalized with COVID-19. Drug-induced fever was suspected and favipiravir was discontinued on Day 10. This preliminary report may help differentiate paradoxical fever in patients receiving favipiravir therapy for COVID-19. Favipiravir for treating patients with novel coronavirus (COVID-19): protocol for a systematic review and meta-analysis of randomised clinical trials Nafamostat mesylate treatment in combination with favipiravir for patients critically ill with Covid-19: A case series abstract: Favipiravir, an antiviral agent, is undergoing clinical trials for treating novel coronavirus disease 2019 (COVID-19). We report two cases of COVID-19 with favipiravir-induced fever. In both cases, pyrexia was observed following administration of favipiravir despite symptoms of COVID-19 improving. No other cause for the fever was evident after careful physical examination and laboratory investigation. Once favipiravir was discontinued, the fever subsided in both patients. To our knowledge, this is the first report of favipiravir-induced fever. url: https://api.elsevier.com/content/article/pii/S1201971220321664 doi: 10.1016/j.ijid.2020.09.1450 id: cord-301079-n1nytr6k author: Tan, Li title: Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China date: 2020-07-27 words: 3556.0 sentences: 205.0 pages: flesch: 60.0 cache: ./cache/cord-301079-n1nytr6k.txt txt: ./txt/cord-301079-n1nytr6k.txt summary: Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Here we collected air and surface samples from isolation wards and ICU units of a tertiary hospital in Wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (IPC) during the COVID-19 pandemic. We also compared environmental contamination of low-and high-touch surfaces, patient hands and PPE of HCP, and the results were also linked to clinical data of sampling patients. Another study found only 1 out of 14 surgical masks worn by mild and severe COVID-19 patients tested positive for SARS-CoV-2 . Environmental contamination of the SARS-CoV-2 viral RNA could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. abstract: Abstract Background Few studies have explored the air and surface contamination by SARS-CoV-2 virus in healthcare settings. Methods We collected air and surface samples from the isolation wards and intensive care units designated for COVID-19 patients. The clinical data and tests result of nasopharyngeal specimens and serum antibodies were also collected from the sampling patients. Results A total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical COVID-19 patients. Only one air sample taken during the intubation procedure tested positive. High-touch surfaces were slightly more likely contaminated by the RNA of the SARS-CoV-2 virus than low-touch surfaces. Contamination rates was slightly higher near severe/critical patients compared to those near mild patients, although not statistically significant (p <0.05). Surface contamination was still found near the patients with both positive IgG and IgM. Conclusions Air and surface contamination of the viral RNA was relatively low in healthcare settings after enhancement of infection prevention and control. Environmental contamination could still be found near seroconverted patients, suggesting the needs of maintaining constant vigilance in healthcare settings to reduce healthcare associated infection during the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32730827/ doi: 10.1016/j.ijid.2020.07.027 id: cord-262017-utvy0i8l author: Tobar Vega, Pool title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date: 2019-06-21 words: 1526.0 sentences: 92.0 pages: flesch: 40.0 cache: ./cache/cord-262017-utvy0i8l.txt txt: ./txt/cord-262017-utvy0i8l.txt summary: title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. Endemic to Southeast Asia, East Asia and China, Talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (Supparatpinyo et al., 1994) . In the U.S. patients with HIV infection usually undergo testing for endemic fungal infections such as Blastomyces, Histoplasma, Coccidioides and Paracoccidioides. To our knowledge, this is the first case reporting systemic mycosis due toTalaromyces marneffei with associated hyponatremia secondary to SIADH and cross-reactivity with Blastomyces and Histoplasma in urine antigen testing. abstract: Talaromyces marneffei is a fungal opportunistic infection usually seen in immunocompromised patients from eastern countries. In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. marneffei. Concomitantly the patient presented with hyponatremia which was deemed to be from SIADH. We present the first case of a patient with T. marneffei cross reactivity with Blastomyces, Histoplasma and SIADH due to pulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/31229614/ doi: 10.1016/j.ijid.2019.06.018 id: cord-260332-tnz6k2z1 author: Tran, Tu Anh title: CT scan does not make a diagnosis of Covid-19: a cautionary case report() date: 2020-09-02 words: 338.0 sentences: 28.0 pages: flesch: 65.0 cache: ./cache/cord-260332-tnz6k2z1.txt txt: ./txt/cord-260332-tnz6k2z1.txt summary: key: cord-260332-tnz6k2z1 title: CT scan does not make a diagnosis of Covid-19: a cautionary case report() Here, we report the clinical case of a 12-year-old girl presenting with flu-like symptoms, cough, anosmia, ageusia, breathing difficulties, patchy ground glass opacities on TDM chest scan who turned out to be Coronavirus 229E-infected. This case must draw attention on the risk of false COVID-19 diagnosis when relying overly on CT scan imaging. RT-PCR assays of nasopharyngeal samples at admittance and 24 hours later, were negative for SARS-CoV-2. In this case report, parents'' anosmia and ageusia as well as chest scanner could have been misleading. According to Kim et al., scanner screening of patients with suspected COVID-19 in low-prevalence countries has a poor positive prediction value (1%-31%) 2 . The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. abstract: Here, we report the clinical case of a 12-year-old girl presenting with flu-like symptoms, cough, anosmia, ageusia, breathing difficulties, patchy ground glass opacities on TDM chest scan who turned out to be Coronavirus 229E-infected. This case must draw attention on the risk of false COVID-19 diagnosis when relying overly on CT scan imaging. url: https://www.ncbi.nlm.nih.gov/pubmed/32890723/ doi: 10.1016/j.ijid.2020.08.073 id: cord-326881-3j2e92dj author: Vassallo, M. title: Patients with Covid-19 exhibit different immunological profiles according to their clinical presentation date: 2020-09-28 words: 2385.0 sentences: 132.0 pages: flesch: 45.0 cache: ./cache/cord-326881-3j2e92dj.txt txt: ./txt/cord-326881-3j2e92dj.txt summary: Conclusions In a population of elderly patients recently infected with Covid-19, CD10 + B cell levels were inversely correlated with clinical severity. However, clinical expression of Covid-19 is extremely variable, with, in some cases, asymptomatic or mild forms [15] , while in other subjects severe forms culminating in acute respiratory distress syndrome (ARDS) have been described, requiring patients to be transferred to Intensive Care Units. The aim of this study was to retrospectively analyze the immunological profile of patients at early stages of Covid-19 in order to identify potential risk factors for subsequent clinical deterioration. We conducted an observational, retrospective cohort study on patients admitted to the Internal Medicine and Infectious Diseases Department in Cannes General Hospital, from March to May 2020, with confirmed Covid-19 infection. In a population of elderly patients at a very early stage of Covid-19, we found that levels of CD10+ B lymphocyte cells were predictive of the clinical severity. abstract: Objectives A novel beta coronavirus has been identified as responsible for the 2019 coronavirus infection (Covid-19). Clinical presentations range from asymptomatic cases to acute respiratory distress syndrome with fatal outcome. Such a broad spectrum of disease expression calls for an investigation of immune response characteristics. Methods We identified subjects admitted for Covid-19 in whom a large panel of immunological markers were measured, including B- and T- and NK-lymphocyte phenotypes, T-lymphocyte subpopulation cells and plasma cytokines. Patients were divided according to symptom severity during hospitalisation, in those with uncomplicated and complicated infection. Differences between groups were analyzed. Results Seventeen patients were included (mean age: 83 years; 9 women; mean delay of symptoms onset: 4 days). Six had uncomplicated infection, while 11 developed complicated forms during the hospitalization. CD10 + B lymphocyte levels were inversely correlated with clinical severity (5.8% vs 2.0%, p = 0.04) and CD10+ levels above 3% were independently associated with uncomplicated forms [Odds Ratio 0.04 (CI 0.002-0.795, p = 0.034)]. TNF-alpha, IL-1, Il-6 and Il-8 measurements upon admission differed between patients who died and those who survived (p < 0.01 for all comparisons). Conclusions In a population of elderly patients recently infected with Covid-19, CD10 + B cell levels were inversely correlated with clinical severity. Cytokine values upon admission were highly predictive of fatal outcome during hospitalisation. These findings could explain differences in the clinical presentation and allow rapid identification of patients at risk for complications. url: https://api.elsevier.com/content/article/pii/S1201971220321548 doi: 10.1016/j.ijid.2020.09.1438 id: cord-306682-01q775up author: Vijgen, Leen title: Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date: 2004-06-22 words: 2965.0 sentences: 166.0 pages: flesch: 54.0 cache: ./cache/cord-306682-01q775up.txt txt: ./txt/cord-306682-01q775up.txt summary: In this study we examined whether polymorphisms could be detected in the HCoV-229E binding domain of APN in a Caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in HCoV-229E attachment to human cells. A total of 100 healthy unrelated Belgian individuals were screened for polymorphisms in the human aminopeptidase N domain that is essential for its HCoV-229E receptor activity. All individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the APN gene. In our search for polymorphisms in the APN domain that is essential for its HCoV-229E receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. Three polymorphisms in APN exon 4 (C956T, G978T and G987A) in association with an intron 3 variation (C389T), were identified at a relatively high allele frequency (8.5%) in our Belgian population. abstract: Objective: Human aminopeptidase N (APN/CD13/ANPEP) has been identified as the receptor for human coronavirus (HCoV) 229E. In this study, we analyzed the region of the APN gene that encodes a stretch of amino acid residues, essential for its HCoV-229E receptor function (amino acids 260–353). Methods: Full-length APN exon 3, intron 3 and exon 4, was PCR-amplified and sequenced in DNA samples from 100 unrelated Caucasian Belgian healthy volunteers. Results: We identified seven polymorphisms, including four intron 3 and three exon 4 variations. Apart from the already known C956T exon 4 mutation, the six other polymorphisms have not yet been described. The most prevalent APN variations in this population (C956T leading to an alanine to valine substitution, G978T, G987A and intron3-C389T) always occurred together at an allele frequency of 8.5%. Haploid DNA sequencing demonstrated the presence of these four variations on the same allele. Three polymorphisms in intron 3, intron3-G395C, intron3-C86T, and intron3-C429T, were identified with an allele frequency of 3.5%, 1% and 0.5% respectively. Five haplotypes were identified in the population of 100 individuals. Conclusion: These results demonstrate that there is a relatively broad spectrum of variations in the APN domain critical for coronavirus binding. The nucleotide sequence reported here has been submitted to the GenBank database with the following accession number: AF527789. url: https://www.ncbi.nlm.nih.gov/pubmed/15234325/ doi: 10.1016/j.ijid.2004.03.004 id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 words: 2771.0 sentences: 166.0 pages: flesch: 51.0 cache: ./cache/cord-302409-40ktyt5q.txt txt: ./txt/cord-302409-40ktyt5q.txt summary: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs'' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. abstract: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. METHODS: Surfaces of objects were routinely wiped with 1000 mg/L chlorine containing disinfectant. Air and sewage disinfection was proceeded routinely and strictly. Hospital environmental surfaces and PPE of staffs in isolation wards were sampled using swabs. The sewage from various inlet and outlets were sampled. The respiratory and stool specimens of patients were collected. The respiratory specimens of staffs in the isolation wards were also sampled once a week. Quantitative real-time reverse transcription PCR (qRT-PCR) methods were used to confirm the existence of SARS-Cov-2 RNA. Viral culture was done for the samples positive for SARS-Cov-2 RNA. RESULTS: During the study period, 33 laboratory-confirmed patients were hospitalized in isolation wards in the hospital. None of SARS-Cov-2 RNA was detected among the 36 objects surface samples and 9 staffs PPE samples in isolation wards. Though the 3 sewage samples from the inlet of preprocessing disinfection pool were positive for SARS-CoV-2 RNA and the sample from the outlet of preprocessing disinfection pool was weakly positive, the sewage sample from the outlet of the last disinfection pool was negative. All of the 5 sewage samples from various points were negative by viral culture of SARS-Cov-2. None of the respiratory specimens of staffs in the isolation wards were positive. CONCLUSIONS: Though SARS-Cov-2 RNA of the sewage samples were positive from inlets of the sewage disinfection pool and negative from the outlet of the last sewage disinfection pool, no viable virus was detected by culture. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. url: https://www.ncbi.nlm.nih.gov/pubmed/32311449/ doi: 10.1016/j.ijid.2020.04.024 id: cord-258881-74aijckl author: Wang, Maomao title: Case Report: One Case of Coronavirus Desease 2019(COVID-19) in Patient Co-nfected by HIV With a Low CD4+ T Cell Count date: 2020-04-23 words: 670.0 sentences: 45.0 pages: flesch: 64.0 cache: ./cache/cord-258881-74aijckl.txt txt: ./txt/cord-258881-74aijckl.txt summary: Abstract The ongoing outbreak of COVID-19 that began in Wuhan, China has become an emergency of international concern When thousands of peolple were infected around the world.We report a case infected by SARS-Cov-2 and HIV simultaneously,which showed a longer course of disease and slower generation of specific antibody. Here we report a patient infected by SARS-Cov-2 , who had a relatively long course of disease with unstable state. Then eight markers of infectious diseases was checked and the result showed that abtibodies to HIV and syphilis were positive .Then the patient was transferred to specialty hospital for further treatment on March 8. People are generally susceptible to SARS-Cov-2 infection, especially the elderly patients and those with underlying diseases [2] . The author suggested that SARS-Cov-2 might damage lymphocytes, especially T lymphocytes, and the immune system was impaired during the period of disease [2] . In conclusion, we report the clinical features of a patient infected by SARS-Cov-2 and HIV. abstract: Abstract The ongoing outbreak of COVID-19 that began in Wuhan, China has become an emergency of international concern When thousands of peolple were infected around the world.We report a case infected by SARS-Cov-2 and HIV simultaneously,which showed a longer course of disease and slower generation of specific antibody. This case highlights the coinfection of SARS-Cov-2 and HIV may impaire the immune system worse. url: https://doi.org/10.1016/j.ijid.2020.04.060 doi: 10.1016/j.ijid.2020.04.060 id: cord-326143-6ndqgxy8 author: Wang, Qiang title: Successful recovery of severe COVID-19 with cytokine storm treating with extracorporeal blood purification date: 2020-05-26 words: 1325.0 sentences: 89.0 pages: flesch: 59.0 cache: ./cache/cord-326143-6ndqgxy8.txt txt: ./txt/cord-326143-6ndqgxy8.txt summary: COVID-19 associated cytokine storm could induce ARDS rapidly and the patients would require the support of mechanic ventilation. We present a case of severe SARS-CoV-2 infection who recovered from cytokine storm. The patients with confirmed COVID-19 progressed to acute respiratory distress syndrome (ARDS) rapidly in an incident rate as high as 41.8% 1 , and many of them require mechanic ventilation. Cytokines could be eliminated effectively by extracorporeal blood purification (EBP) 4 , which thus could interrupt the initiation and progression of inflammation cascade in the scenario of COVID-19. IL-6 (198.66 pg/ml) was almost 10 folds of normal range (≤5.9 pg/ml) which indicated an initiation of cytokine storm on day 12 ( Figure 1 ). The patient was largely stable until the chest distress exacerbated and blood in phlegm developed on day 14. Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease abstract: COVID-19 associated cytokine storm could induce ARDS rapidly and the patients would require the support of mechanic ventilation. However, the prognosis was not that optimistic. The outcome might be changed if the intervention of EBP was performed timely. We present a case of severe SARS-CoV-2 infection who recovered from cytokine storm. url: https://www.sciencedirect.com/science/article/pii/S1201971220303726?v=s5 doi: 10.1016/j.ijid.2020.05.065 id: cord-280627-dfnc9g2c author: Wang, Xiong title: Comparison of nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 words: 1846.0 sentences: 111.0 pages: flesch: 53.0 cache: ./cache/cord-280627-dfnc9g2c.txt txt: ./txt/cord-280627-dfnc9g2c.txt summary: The diagnosis of COVID-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of SARS-CoV-2 from numerous types of specimens. However, negative oropharyngeal and nasopharyngeal swabs could not rule out COVID-19, as some patients got positive SARS-CoV-2 from other types of specimen, including bronchoalveolar lavage fluid J o u r n a l P r e -p r o o f (BALF), anal swab, stool, and urine 12, 13 . We reviewed the medical record from February 16, 2020 to March 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in SARS-CoV-2 detection from 353 patients who received tests with both specimens simultaneously. Respiratory tract specimen was suggested for SARS-CoV-2 RT-PCR test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (BALF). abstract: Abstract Background Since the outbreak of coronavirus disease (COVID-19) in Wuhan in December 2019, by March 10, 2020, a total of 80,932 confirmed cases have been reported in China. Two consecutively negative RT-PCR test results in respiratory tract specimens is required for the evaluation of discharge from hospital, and oropharyngeal swabs were the most common sample. However, false negative results occurred in the late stage of hospitalization, and avoiding false negative result is critical essential. Methods We reviewed the medical record of 353 patients who received tests with both specimens simultaneously, and compared the performance between nasopharyngeal and oropharyngeal swabs. Results Of the 353 patients (outpatients, 192; inpatients, 161) studied, the median age was 54 years, and 177 (50.1%) were women. Higher positive rate (positive tests/total tests) was observed in nasopharyngeal swabs than oropharyngeal swabs, especially in inpatients. Nasopharyngeal swabs from inpatients showed higher positive rate than outpatients. Nasopharyngeal swabs from male showed higher positive rate than female, especially in outpatients. Detection with both specimens slightly increased the positive rate than nasopharyngeal swab only. Moreover, the consistency between from nasopharyngeal and oropharyngeal swabs were poor (Kappa=0.308). Conclusion In conclusion, our study suggests that nasopharyngeal swabs may be more suitable than oropharyngeal swab at this stage of COVID-19 outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/32315809/ doi: 10.1016/j.ijid.2020.04.023 id: cord-290100-wnjjqqn5 author: Wong, Samuel Y.S. title: Primary care physicians’ response to pandemic influenza in Hong Kong: a mixed quantitative and qualitative study date: 2012-07-11 words: 3951.0 sentences: 186.0 pages: flesch: 52.0 cache: ./cache/cord-290100-wnjjqqn5.txt txt: ./txt/cord-290100-wnjjqqn5.txt summary: OBJECTIVES: The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. RESULTS: We found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among GOPC doctors during the study period. The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. abstract: OBJECTIVES: The current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza A H1N1 virus in Hong Kong in 2009. METHODS: A cross-sectional survey was conducted of 300 doctors working in public primary care clinics. In addition, a qualitative study was conducted in two selected general outpatient clinics (GOPCs) with 10 doctors between September and December 2009. RESULTS: We found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among GOPC doctors during the study period. CONCLUSIONS: Since hand hygiene and influenza vaccination are effective methods to prevent the spread of influenza infection, future studies should explore the reasons for non-compliance with these preventive behaviors among doctors. More education and training in dealing with influenza A H1N1 infection may be needed. url: https://www.sciencedirect.com/science/article/pii/S1201971212011794 doi: 10.1016/j.ijid.2012.03.015 id: cord-257737-obadq502 author: Wu, Di title: Positive effects of COVID-19 control measures on influenza prevention date: 2020-04-10 words: 354.0 sentences: 31.0 pages: flesch: 75.0 cache: ./cache/cord-257737-obadq502.txt txt: ./txt/cord-257737-obadq502.txt summary: title: Positive effects of COVID-19 control measures on influenza prevention This article aims to alert clinicians of the presence of co-infection with these two viruses and to describe the effect of the measures taken to fight COVID-19 on influenza prevention and control. [ 4 ] have reported the case of a patient co-infected with SARS-CoV-2 and influenza A virus. Also, Li and Wang [ 5 ] have reported the need to be alert to the superposed effect of seasonal influenza while fighting pneumonia caused by the novel coronavirus. Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention Coronavirus disease 2019 (COVID-19) Situation Report -71 Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia Be alert to superposed effect of seasonal influenza while fighting against novel coronavirus pneumonia abstract: Abstract Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now become a pandemic threat to the whole world. At the same time, influenza virus has been active, with influenza virus and SARS-CoV-2 sharing the same transmission routes. This article aims to alert clinicians of the presence of co-infection with these two viruses and to describe the effect of the measures taken to fight COVID-19 on influenza prevention and control. url: https://doi.org/10.1016/j.ijid.2020.04.009 doi: 10.1016/j.ijid.2020.04.009 id: cord-275250-ilmgy7ce author: Xia, Yong title: Dynamics of antibodies to SARS-CoV-2 in a case with SARS-CoV-2 infection date: 2020-05-17 words: 728.0 sentences: 52.0 pages: flesch: 63.0 cache: ./cache/cord-275250-ilmgy7ce.txt txt: ./txt/cord-275250-ilmgy7ce.txt summary: As shown in Table 1 , on Feb 14, reactivity to IgM/ IgG antibodies was very weak and invisible to the naked eye by using Kit A, C. Reactivity to IgM was also higher than that detected by using Kit B and C on Feb 17, respectively. Furthermore, IgM and IgG antibody levels were 0.92 AU/mL, 13.46 AU/mL, respectively, which was higher than that detected by using Kit D on Feb 17 (Figure 1 ). In the present study, IgG/IgM antibodies to specific proteins of SARS-CoV-2 were found in blood sample of the patient and gradually increased. Because COVID-19 is a newly emerged disease, the patient with either positive for IgM or IgG antibodies to SARS-CoV-2 should be considered as the presence of SARS-CoV-2 infection. So we believe that positive for IgM or IgG antibodies could be a marker to diagnosis of SARS-CoV-2 infection no matter the results of testing nucleic acid. abstract: nan url: https://api.elsevier.com/content/article/pii/S1201971220303490 doi: 10.1016/j.ijid.2020.05.042 id: cord-279976-juz9jnfk author: Xie, Mingxuan title: Insight into 2019 novel coronavirus — an updated intrim review and lessons from SARS-CoV and MERS-CoV date: 2020-04-01 words: 3863.0 sentences: 228.0 pages: flesch: 50.0 cache: ./cache/cord-279976-juz9jnfk.txt txt: ./txt/cord-279976-juz9jnfk.txt summary: METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Chinese Center for Disease Control and Prevention (CCDC) identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Gorbalenya et al., 2020) , that responsible for the pandemic. Further search words were above keywords, "SARS" OR "SARS-CoV" OR "severe acute respiratory syndrome", "MERS" OR "MERS-CoV" OR "middle east respiratory syndrome", in combinations of with "spike protein" OR "genome" OR "reproductive number" OR "incubation period" OR "serial interval" OR "fatality rate" OR "clinical characteristics" OR "pathology" OR "autopsy" OR "treatment". abstract: BACKGROUND: The rapid spread of the coronavirus disease 2019 (COVID-19), caused by a zoonotic beta-coronavirus entitled 2019 novel coronavirus (2019-nCoV), has become a global threat. Awareness of the biological features of 2019-nCoV should be updated in time and needs to be comprehensively summarized to help optimize control measures and make therapeutic decisions. METHODS: Based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-nCoV infection, in comparison with severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV) infection. RESULTS: The genome of 2019-nCoV partially resembled SARS-CoV and MERS-CoV, and indicating a bat origin. The COVID-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than SARS and MERS. Clinical presentation and pathology of COVID-19 greatly resembled SARS and MERS, with less upper respiratory and gastrointestinal symptoms, and more exudative lesions in post-mortems. Potential treatments included remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). CONCLUSION: The initial experience from the current pandemic and lessons from the previous two pandemics can help improve future preparedness plans and combat disease progression. url: https://www.sciencedirect.com/science/article/pii/S1201971220302046?v=s5 doi: 10.1016/j.ijid.2020.03.071 id: cord-347349-caz5fwl1 author: Yu, Xinhua title: Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea date: 2020-07-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Elderly people had suffered disproportional burden of COVID-19. We hypothesized that males and females in different age groups might have different epidemic trajectories. METHODS: Using publicly available data from South Korea, daily new COVID-19 cases were fitted with generalized additive models, assuming Poisson and negative binomial distributions. Epidemic dynamics by age and gender groups were explored with interactions between smoothed time terms and age and gender. RESULTS: A negative binomial distribution fitted the daily case counts best. Interaction between the dynamic patterns of daily new cases and age groups was statistically significant (p < 0.001), but not with gender group. People aged 20-39 years led the epidemic processes in the society with two peaks: one major peak around March 1 and a smaller peak around April 7, 2020. The epidemic process among people aged 60 or above was trailing behind that of younger people with smaller magnitude. After March 15, there was a consistent decline of daily new cases among elderly people, despite large fluctuations of case counts among young adults. CONCLUSIONS: Although young people drove the COVID-19 epidemic in the whole society with multiple rebounds, elderly people could still be protected from virus infection after the peak of epidemic. url: https://www.sciencedirect.com/science/article/pii/S1201971220305361?v=s5 doi: 10.1016/j.ijid.2020.06.101 id: cord-320860-qt84oicg author: Zhang, Aining title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 date: 2020-09-15 words: 2359.0 sentences: 131.0 pages: flesch: 47.0 cache: ./cache/cord-320860-qt84oicg.txt txt: ./txt/cord-320860-qt84oicg.txt summary: title: Meta-Analysis of coagulation parameters associated with disease severity and poor prognosis of COVID-19 However, a recent study suggested that the characteristics of COVID-19-associated J o u r n a l P r e -p r o o f coagulopathy(CAC) are different from clotting disorders caused by bacterial infections and other diseases. In order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among COVID-19 patients. Our exclusion criteria included (1) asymptomatic patients; J o u r n a l P r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Procalcitonin in patients with severe coronavirus disease 2019 (COVID-19): A meta-analysis abstract: Background To figure out whether abnormal coagulation parameters are associated with disease severity and poor prognosis in patients with 2019 Corona Virus Disease (COVID-19). Methods A systematic literature search was conducted using the databases PubMed, Embase, and Web of sciences until April 25, 2020. We included a total of 15 studies with 2277 patients. Platelet count (PLT), prothrombin time (PT), activated partial thromboplastin time (APTT), D-dimer (D-D) and fibrinogen (FIB) were collected and analyzed. The statistical results were expressed the effect measure by mean difference (MD) with the related 95% confidence interval (CI). Results The PLT level of severe patients was lower than that of mild patients, while the levels of PT, D-D and FIB were higher than those of mild patients (P < 0.05). The level of APTT had no statistical difference between two groups (P > 0.05). Compared to Non-ICU patients, PT of ICU patients was significantly longer (P < 0.05). In Non-survivors, PT and D-D were higher, yet PLT was lower than survivors (P < 0.05). There was no significant difference in APTT between survivors and Non-survivors (P > 0.05). The funnel plot and Egger's Regression test demonstrated that there was no publication bias. Conclusions Our data support the notion that coagulopathy could be considered as a risk factor for disease severity and mortality of COVID-19, which may help clinicians to identify the incidence of poor outcomes in COVID-19 patients. url: https://www.sciencedirect.com/science/article/pii/S1201971220307372?v=s5 doi: 10.1016/j.ijid.2020.09.021 id: cord-282360-byqhzyzi author: Zhang, Dingmei title: Enterovirus 71 vaccine: close but still far date: 2010-04-18 words: 4404.0 sentences: 248.0 pages: flesch: 43.0 cache: ./cache/cord-282360-byqhzyzi.txt txt: ./txt/cord-282360-byqhzyzi.txt summary: To overcome the potential problem of reversion to virulence of attenuated strain vaccine, subunit vaccines consisting of only one or a few ''subunit'' proteins of the pathogen that can stimulate immune responses directed at the intact virus have been developed using recombinant DNA technology. 21 have described a recombinant VP1 protein expressed in Escherichia coli BL21, showing that the VP1 protein with a complete adjuvant is able to elicit a neutralizing antibody response, enhance T helper cell proliferation, and induce high levels of interleukin (IL)-10 and interferon (IFN)-g in mice, providing direct evidence that the VP1 protein contains neutralizing epitopes independent of other viral capsid proteins; this paves the way for the use of VP1 as a backbone antigen for developing subunit vaccines against EV71. Protection against lethal enterovirus 71 infection in newborn mice by passive immunization with subunit VP1 vaccines and inactivated virus abstract: BACKGROUND: Enterovirus 71 (EV71), a member of the Enterovirus genus of the Picornaviridae family, is one of the causative pathogens of hand-foot-and-mouth disease (HFMD) and the most common etiological agent isolated from HFMD patients complicated with neurological disorders. EV71 has become an increasingly important neurotropic enterovirus in the post-poliomyelitis eradication era. Effective antiviral agents and vaccines against this virus are currently still under development. We reviewed publications on the development of EV71 vaccines in order to provide an overview of the field. METHODS: Fifty-five articles on EV71 vaccine development, published from 1974 to 2009, were collected from Sun Yat-sen University library and reviewed. RESULTS: Various types of vaccine have been developed for EV71. In results published to date, all vaccines for EV71 under development appear to elicit an immune response in rodents or in monkeys. According to the established regulatory standards, it may be relatively easy to acquire a license to use the inactivated virus in order to meet the immediate demands for EV71 control . With regard to the attenuated vaccine, it is critical to increase the genetic stability before clinical use, due to the risk of virulent revertants. The virus-like particle (VLP) vaccine, not only conserving the conformational epitopes, but also having no risk of virulent revertants, is another promising vaccine candidate for EV71, but needs further development. The VP1 capsid protein is the backbone antigen protein for developing subunit vaccine and epitope vaccine; these remain viable potential vaccine strategies worthy of further study and development. CONCLUSIONS: The conservation of the three-dimensional structure is important for the EV71 inactivated vaccine and VLP vaccine to induce a strong immune response. To develop EV71 vaccines with a high protection efficacy, strategies such as the use of adjuvant, strong promoters, tissue-specific promoters, and addition of mucosal immune adjuvant should be considered. url: https://www.ncbi.nlm.nih.gov/pubmed/20400350/ doi: 10.1016/j.ijid.2009.12.002 id: cord-319814-tyqb473m author: Zhang, Dingmei title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 words: 3480.0 sentences: 208.0 pages: flesch: 51.0 cache: ./cache/cord-319814-tyqb473m.txt txt: ./txt/cord-319814-tyqb473m.txt summary: METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. abstract: BACKGROUND: The World Health Organization (WHO) ranks respiratory tract infection (RTI) as the second leading cause of death worldwide for children under 5 years of age. The aim of this work was to evaluate the epidemiology characteristics of respiratory viruses found in children and adults with RTI from July 2009 to June 2012 in southern China. METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. RESULTS: The demographic characteristics, viral prevalence, age distribution, seasonal distribution, and pathogen spectrum of the patients with RTIs were analyzed. Co-infection was observed in 483 specimens, but it was more common in male patients, inpatients, children, and young adults. It varied by season, being more prevalent in the spring and summer and less so in the winter. Human coronavirus and human bocavirus were the most common pathogens, tending to occur in co-infection with other respiratory viruses. CONCLUSIONS: This work adds to our knowledge of the epidemiology characteristics of these seven common respiratory viruses among patients with RTI in southern China. The detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection, and might also provide data relevant to the development of prevention strategies. url: https://api.elsevier.com/content/article/pii/S1201971214014581 doi: 10.1016/j.ijid.2014.02.019 id: cord-297829-aynigoud author: Zhang, Li title: Post-pandemic assessment of public knowledge, behavior, and skill on influenza prevention among the general population of Beijing, China date: 2014-04-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The aim of this study was to assess the knowledge, behavioral, and skill responses toward influenza in the general population of Beijing after pandemic influenza A (H1N1) 2009. METHODS: A cross-sectional study was conducted in Beijing, China, in January 2011. A survey was conducted in which information was collected using a standardized questionnaire. A comprehensive evaluation index system of health literacy related to influenza was built to evaluate the level of health literacy regarding influenza prevention and control among residents in Beijing. RESULTS: Thirteen thousand and fifty-three valid questionnaires were received. The average score for the sum of knowledge, behavior, and skill was 14.12 ± 3.22, and the mean scores for knowledge, behavior, and skill were 4.65 ± 1.20, 7.25 ± 1.94, and 2.21 ± 1.31, respectively. The qualified proportions of these three sections were 23.7%, 11.9%, and 43.4%, respectively, and the total proportion with a qualified level was 6.7%. There were significant differences in health literacy level related to influenza among the different gender, age, educational level, occupational status, and location groups (p < 0.05). There was a significant association between knowledge and behavior (r = 0.084, p < 0.001), and knowledge and skill (r = 0.102, p < 0.001). CONCLUSIONS: The health literacy level remains low among the general population in Beijing and the extent of relativities in knowledge, behavior, and skill about influenza was found to be weak. Therefore, improvements are needed in terms of certain aspects, particularly for the elderly and the population of rural districts. Educational level, as a significant factor in reducing the spread of influenza, should be considered seriously when intervention strategies are implemented. url: https://doi.org/10.1016/j.ijid.2014.01.003 doi: 10.1016/j.ijid.2014.01.003 id: cord-274230-old0xmcc author: Zhao, Qianwen title: Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis date: 2020-05-04 words: 867.0 sentences: 72.0 pages: flesch: 56.0 cache: ./cache/cord-274230-old0xmcc.txt txt: ./txt/cord-274230-old0xmcc.txt summary: title: Lymphopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A systemic review and meta-analysis Mean difference (MD) of lymphocyte count in COVID-19 patients with or without severe disease and odds ratio (OR) of lymphopenia for severe form of COVID-19 was evaluated with this meta-analysis. The pooled analysis showed that lymphocyte count was significantly lower in severe COVID-19 patients (MD -0.31×109/L; 95%CI: -0.42 to -0.19×109/L). After the significant clinical heterogeneity was excluded, the 130 randomized effects model was used for meta-analysis. Severe Outcomes Among Patients with Coronavirus Disease 2019 (COVID-19) -United States Risk Factors Associated With Acute Respiratory Distress Syndrome 284 and Death in Patients With Coronavirus Disease Retrospective study on the epidemiological 300 characteristics of 139 patients with novel coronavirus pneumonia on the effects of Severity Effects of severe acute respiratory syndrome (SARS) coronavirus 311 infection on peripheral blood lymphocytes and their subsets Lymphopenia predicts disease severity of COVID-19: a 322 descriptive and predictive study abstract: Abstract Objectives Coronavirus Disease 2019 (COVID-19) is a new respiratory and systemic disease which needs quick identification of potential critical patients. This meta-analysis aimed to explore the relationship between lymphocyte count and the severity of COVID-19. Methods Comprehensive systematic literature search was carried out to find studies published from December 2019 to 22 March 2020 from five Databases. The language of literatures included English and Chinese. Mean difference (MD) of lymphocyte count in COVID-19 patients with or without severe disease and odds ratio (OR) of lymphopenia for severe form of COVID-19 was evaluated with this meta-analysis. Results Overall 13 case-series with a total of 2282 cases were included in the study. The pooled analysis showed that lymphocyte count was significantly lower in severe COVID-19 patients (MD -0.31×109/L; 95%CI: -0.42 to -0.19×109/L). The presence of lymphopenia was associated with nearly threefold increased risk of severe COVID-19 (Random effects model, OR=2.99, 95% CI: 1.31-6.82). Conclusions Lymphopenia is a prominent part of severe COVID-19 and a lymphocyte count of less than 1.5×109/L may be useful in predicting the severity clinical outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/32376308/ doi: 10.1016/j.ijid.2020.04.086 id: cord-287209-hkrarxsd author: Zhao, Shi title: The basic reproduction number of novel coronavirus (2019-nCoV) estimation based on exponential growth in the early outbreak in China from 2019 to 2020: A reply to Dhungana date: 2020-02-20 words: 941.0 sentences: 65.0 pages: flesch: 66.0 cache: ./cache/cord-287209-hkrarxsd.txt txt: ./txt/cord-287209-hkrarxsd.txt summary: title: The basic reproduction number of novel coronavirus (2019-nCoV) estimation based on exponential growth in the early outbreak in China from 2019 to 2020: A reply to Dhungana The estimates on the basic reproduction number, R0, were carried out in early outbreak as of January 22, 2020 when the surveillance data and the knowledge on the key epidemiological features of 2019-nCoV were limited. The estimates of the basic reproduction number, R0, with varying reporting rates, mean and SD of serial interval (SI). Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak abstract: nan url: https://doi.org/10.1016/j.ijid.2020.02.025 doi: 10.1016/j.ijid.2020.02.025 id: cord-257265-lkzytud0 author: Zheng, Fang title: SARS-CoV-2 Clearance in COVID-19 Patients with Novaferon Treatment: A Randomized, Open-label, Parallel Group Trial date: 2020-08-03 words: 4181.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-257265-lkzytud0.txt txt: ./txt/cord-257265-lkzytud0.txt summary: According to the published information in a US patent (US 7, 625, 555 B2) , this novel protein molecule was created by modified DNA shuffling technology using cDNA sequences of 12 human interferon subtypes as models, and named as Novaferon by its inventors (Wang et al., 2011) .In addition to the human interferon-like physiological functions, Novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (Li et al.,2014) .Novaferon has been shown to enhance and improve the negative conversion of serum HBeAg in clinical studies (Daxianet al.,2015) , and in April 2018, was approved in China for treatment of chronic hepatitis B by former CFDA (Chinese Food and Drug Administration). We first determined whether Novaferon was able to inhibit J o u r n a l P r e -p r o o f SARS-CoV-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of Novaferon in COVID-19patients by observing the SARS-CoV-2 clearance rates. abstract: BACKGROUND: The anti-viral effects of Novaferon, a potent antiviral protein drug on COVID-19 was evaluated in laboratory, and in a randomized, open-label, parallel group trial. METHODS: In laboratory, the inhibition of Novaferon on viral replication in cells infected with SARS-CoV-2, and on prevention of SARS-CoV-2 entry into healthy cells was determined. Antiviral effects of Novaferon in COVID-19 patients with treatment of Novaferon, Novaferon plus Lopinavir/Ritonavir, or Lopinavir/Ritonavir were evaluated. The primary endpoint was the SARS-CoV-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to SARS-CoV-2 clearance. RESULTS: Novaferon inhibited the viral replication (EC(50) = 1.02 ng/ml), and prevented viral infection (EC(50) = 0.10 ng/ml). Results from the 89 enrolled COVID-19 patients showed that both Novaferon and Novaferon plus Lopinavir/Ritonavir groups had significantly higher viral clearance rates on day 6than Lopinavir/Ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). Median time to viral clearance were 6 days, 6 days, and 9 days for three groups respectively, a 3-dayreductionin both Novaferon and Novaferon plus Lopinavir/Ritonavir groups compared with Lopinavir/Ritonavir group. CONCLUSIONS: Novaferon exhibited anti-SARS-CoV-2 effects in vitro and in COVID-19 patients. These data justified the further evaluation of Novaferon. TRIAL REGISTRATION NUMBER: number ChiCTR2000029496at the Chinese Clinical Trial Registry (http://www.chictr.org.cn/). url: https://www.ncbi.nlm.nih.gov/pubmed/32758689/ doi: 10.1016/j.ijid.2020.07.053 id: cord-309032-idjdzs97 author: Zhou, Feng title: Epidemiological Characteristics and Factors Associated with Critical Time Intervals of COVID-19 in Eighteen Provinces, China: A Retrospective Study date: 2020-10-09 words: 4176.0 sentences: 237.0 pages: flesch: 54.0 cache: ./cache/cord-309032-idjdzs97.txt txt: ./txt/cord-309032-idjdzs97.txt summary: Several studies conducted in China, Italy and the United States have reported some epidemiological characteristics of COVID-19 in the initial phase (Grasselli et al., 2020 , Liang et al., 2020 , Price-Haywood et al., 2020 , Richardson et al., 2020 , Wu and McGoogan, 2020 , However, there is still a lack of research on the space-time characteristics in the populations of imported and local cases respectively which is of great significance. In this study, we described the spatiotemporal distribution of the COVID-19 in eighteen provinces of China (outside Hubei province) and investigated the epidemiological characteristics in the population of imported cases and local cases, from the beginning of this epidemic until it was under good control. We further assessed the critical influence factors associated with time interval from symptom onset to hospitalization (TOH) and length of hospital stay (LOS), including demographic and temporal and spatial characteristics. abstract: Background As COVID-19 ravages continuously around the world, more information on the epidemiological characteristics and factors associated with time interval between critical events is needed to contain the pandemic and to assess the effectiveness of interventions. Methods Individual information on confirmed cases from January 21 to March 2 was collected from provincial or municipal health commissions. We identified the difference between imported and local cases in the epidemiological characteristics. Two models were established to estimate the factors associated with time interval from symptom onset to hospitalization (TOH) and length of hospital stay (LOS) respectively. Results Among 7,042 cases, 3392 (48.17%) were local cases and 3304 (46.92%) were imported cases. Since the first intervention was adopted in Hubei on January 23, the daily reported imported cases reached a peak on January 28 and gradually decreased since then. Imported cases were on average younger (41 vs. 48), and had more male (58.66% vs. 47.53%) compared to local cases. Furthermore, imported cases had more contacts with other confirmed cases (2.80 ± 2.33 vs. 2.17 ± 2.10), which were mainly within family members (2.26 ± 2.18 vs. 1.57 ± 2.06). The TOH and LOS were 2.67 ± 3.69 and 18.96 ± 7.63 days respectively, and a longer TOH was observed in elderly living in the provincial capital cities that were higher migration intensity with Hubei. Conclusions Measures to restrict traffic can effectively reduce imported spread. However, household transmission is still not controlled, particularly for the infection of imported cases to elderly women. It is still essential to surveil and educate patients about the early admission or isolation. url: https://www.ncbi.nlm.nih.gov/pubmed/33045428/ doi: 10.1016/j.ijid.2020.09.1487 id: cord-257200-q0vqlerz author: Zumla, A. title: What is the experience from previous mass gathering events? Lessons for Zika virus and the Olympics 2016 date: 2016-06-15 words: 2506.0 sentences: 133.0 pages: flesch: 52.0 cache: ./cache/cord-257200-q0vqlerz.txt txt: ./txt/cord-257200-q0vqlerz.txt summary: 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. 5 All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. The spread of severe acute respiratory syndrome coronavirus (SARS-CoV) from China to Hong Kong and further to Canada was not due to a mass gathering, but to infected individuals travelling late in the incubation period or just after the onset of symptoms. A review in this issue discusses the need for vaccines for mass gatherings and draws attention to immunization against pneumococcal infections in elderly pilgrims and highlights that polio may be a risk. Communicable diseases as health risks at mass gatherings other than Hajj: what is the evidence? abstract: All previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis A, polio and meningitis. Three mass gathering held in Africa during the Ebola outbreak accepted participants from West Africa and was able to handle the theoretical risk without any incident. Therefore we believe that the Olympic games in Rio de Janeiro should not be cancelled. The number of visitors to the games is a tiny fraction (1%) of other visitors to Zika endemic countries and it will have no measurable effect on the risk of spreading Zika virus, if the games was cancelled. url: https://www.sciencedirect.com/science/article/pii/S1201971216310943 doi: 10.1016/j.ijid.2016.06.010 id: cord-260518-mswb3q67 author: Zumla, Alimuddin title: Taking forward a ‘One Health’ approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential date: 2016-06-15 words: 4039.0 sentences: 188.0 pages: flesch: 43.0 cache: ./cache/cord-260518-mswb3q67.txt txt: ./txt/cord-260518-mswb3q67.txt summary: Since the Kingdom of Saudi Arabia is host to millions of pilgrims each year travelling from all continents, 29 tackling the threat of MERS and other infectious diseases with epidemic potential will require enhanced closer cooperation between those who provide human health, animal health, and environmental health services, locally, nationally, regionally, and internationally: the Middle Eastern, European, African, Asian, and American governments, veterinary groups, the WHO, the Food and Agriculture Organization (FAO), the African Union, the United Nations International Children''s Emergency Fund (UNICEF), The World Bank, Office International des Epizooties (OIE), CDC, Public Health England, the newly formed Africa CDC, and funding agencies among others. The persistence of MERS-CoV 4 years since its first discovery has created major opportunities for each of the Middle Eastern and African countries to take leadership of the ''One Health'' approach with a view to bringing this under regional and global umbrellas, to tackle new emerging and re-emerging infectious diseases with epidemic potential. abstract: The appearance of novel pathogens of humans with epidemic potential and high mortality rates have threatened global health security for centuries. Over the past few decades new zoonotic infectious diseases of humans caused by pathogens arising from animal reservoirs have included West Nile virus, Yellow fever virus, Ebola virus, Nipah virus, Lassa Fever virus, Hanta virus, Dengue fever virus, Rift Valley fever virus, Crimean-Congo haemorrhagic fever virus, severe acute respiratory syndrome coronavirus, highly pathogenic avian influenza viruses, Middle East Respiratory Syndrome Coronavirus, and Zika virus. The recent Ebola Virus Disease epidemic in West Africa and the ongoing Zika Virus outbreak in South America highlight the urgent need for local, regional and international public health systems to be be more coordinated and better prepared. The One Health concept focuses on the relationship and interconnectedness between Humans, Animals and the Environment, and recognizes that the health and wellbeing of humans is intimately connected to the health of animals and their environment (and vice versa). Critical to the establishment of a One Health platform is the creation of a multidisciplinary team with a range of expertise including public health officers, physicians, veterinarians, animal husbandry specialists, agriculturalists, ecologists, vector biologists, viral phylogeneticists, and researchers to co-operate, collaborate to learn more about zoonotic spread between animals, humans and the environment and to monitor, respond to and prevent major outbreaks. We discuss the unique opportunities for Middle Eastern and African stakeholders to take leadership in building equitable and effective partnerships with all stakeholders involved in human and health systems to take forward a ‘One Health’ approach to control such zoonotic pathogens with epidemic potential. url: https://www.sciencedirect.com/science/article/pii/S1201971216310967 doi: 10.1016/j.ijid.2016.06.012 id: cord-291367-rtmsrh16 author: Zumla, Alimuddin title: Middle East Respiratory Syndrome - need for increased vigilance and watchful surveillance for MERS-CoV in sub-Saharan Africa date: 2015-07-02 words: 2262.0 sentences: 119.0 pages: flesch: 50.0 cache: ./cache/cord-291367-rtmsrh16.txt txt: ./txt/cord-291367-rtmsrh16.txt summary: 4, 5 The recent unprecedented outbreak of the MERS 6, 7 in South Korea which arose consequential to the importation of MERS-CoV by a South Korean traveler to the Middle East, alarmed global public health authorities and highlights the potential of MERS-CoV to spread across the globe and cause local outbreaks. National surveillance systems should be on alert for the low but long-lasting risk of MERS-CoV infected pilgrims returning from the Umrah throughout the year, and also for the large numbers of refugees at several conflict zones in the Middle East (those migrating from Syria to Turkey and from the Yemen border into Saudi Arabia and beyond). The Hajj pilgrimage and surveillance for Middle East Respiratory syndrome coronavirus in pilgrims from African countries Infection prevention and control during health care for probable or confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. abstract: nan url: https://doi.org/10.1016/j.ijid.2015.06.020 doi: 10.1016/j.ijid.2015.06.020 id: cord-292988-q1yz9y8k author: Zumla, Alimuddin title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy - achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 words: 3157.0 sentences: 174.0 pages: flesch: 39.0 cache: ./cache/cord-292988-q1yz9y8k.txt txt: ./txt/cord-292988-q1yz9y8k.txt summary: title: Reducing mortality and morbidity in patients with severe COVID-19 disease by advancing ongoing trials of Mesenchymal Stromal (stem) Cell (MSC) therapy achieving global consensus and visibility for cellular host-directed therapies We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. It appears that all three lethal zoonotic coronaviruses, MERS-CoV, SARS-CoV and SARS-CV-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ARDS) Li G et al, 2020; Li G et al, 2020) . abstract: Abstract As of May 11th 2020, the coronavirus disease 2019 (COVID-19) pandemic, caused by the novel, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused 274,361 deaths out of 3,917,366 (7% case fatality rate). As with the two other novel coronavirus zoonotic diseases of humans, SARS and MERS, no specific treatments for reducing mortality or morbidity are yet available. Deaths from COVID-19 will continue to rise globally until effective and appropriate treatments and vaccines are found. With no specific treatments being available for treating COVID-19 patients, the global medical, scientific, pharma and funding communities have rapidly initiated over 500 COVID-19 clinical on a range of antiviral drug regimens, biologics, repurposed drugs in various combinations. We focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (Stem) cells (MSCs) in treatment trials of patients with severe COVID-19 disease. This is an area which has been eclipsed by the current emphasis the huge number of trials evaluating new anti-viral drugs, repurposed drugs and combinations thereof. MSCs should also be trialed for treatment of severe cases of MERS where mortality rates are upto 34% and MERS-CoV remains a WHO priority Blueprint pathogen. It’s about time funding agencies now invest more into development MSCs per se and other host-directed therapies in combination with other therapeutic interventions. MSC therapy could turn out to be an important contribution to bringing an end to the high COVID-19 and MERS death rates. url: https://doi.org/10.1016/j.ijid.2020.05.040 doi: 10.1016/j.ijid.2020.05.040 id: cord-311654-ixn65hxb author: Zumla, Alimuddin title: COVID-19 and the scaled-down 2020 Hajj Pilgrimage - Decisive, logical and prudent decision making by Saudi authorities overcomes pre-Hajj public health concerns date: 2020-08-08 words: 1417.0 sentences: 74.0 pages: flesch: 54.0 cache: ./cache/cord-311654-ixn65hxb.txt txt: ./txt/cord-311654-ixn65hxb.txt summary: Apart from generic prevention and control issues of public health and lockdown measures to limit epidemic spread, specific issues of Mass Gathering (MG) sporting and religious events came under specific spotlight (Alzahrani et al, 2020; Baloch et al, 2020; McCloskey et al, 2020; . WHO with global MG partners, developed comprehensive key recommendations for COVID-19, and since end of February, 2020, there was a stepwise increase in cancellation, temporary suspension or postponement of international and national religious, sporting, musical, and other MGs, as countries worldwide took public health and other measures (WHO, 2020b; McCloskey et al, 2020; Petersen, McCloskey et al, 2020) . The successful completion of the 2020 Hajj is a major tribute to the leadership and commitment of the Saudi authorities, and it reflects their extensive experience of organising the annual Hajj pilgrimage, and continued commitment to improvement public health issues related to mass gatherings events. abstract: nan url: https://api.elsevier.com/content/article/pii/S1201971220306433 doi: 10.1016/j.ijid.2020.08.014 id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 words: 1791.0 sentences: 101.0 pages: flesch: 41.0 cache: ./cache/cord-334603-yt2pmxi3.txt txt: ./txt/cord-334603-yt2pmxi3.txt summary: title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. abstract: Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. Ethnicity has been the focus of attention after data from the United Kingdom showed a disproportionate number of deaths among healthcare workers from black, Asian and other ethnic minority backgrounds (1). In addition to ethnicity, socio-economic factors, prior vaccinations and exposure to other coronaviruses, other factors need to be considered to explain geographical and regional variations in susceptibility, severity of clinical expression of COVID-19 disease and outcomes. In the United States there have been disproportionate COVID-19 death rates among African Americans at around 2.6 times higher than that of other groups. Although these data could be due to multiple cultural and socioeconomic factors an underlying genetic susceptibility to SARS-CoV-2 infection may be a factor. url: https://doi.org/10.1016/j.ijid.2020.07.016 doi: 10.1016/j.ijid.2020.07.016 id: cord-303417-1237ykxt author: d’Arminio Monforte, Antonella title: Effectiveness of Hydroxychloroquine in COVID-19 disease: A done and dusted situation? date: 2020-07-29 words: 659.0 sentences: 42.0 pages: flesch: 52.0 cache: ./cache/cord-303417-1237ykxt.txt txt: ./txt/cord-303417-1237ykxt.txt summary: Arshad et al show evidence for a reduced mortality in Covid-19 patients taking hydroxychloroquine alone or with azithromycin in an observational study in USA [1] . We divided a subset of our cohort in three groups who started treatment a median of 1 day after admission: those receiving hydroxycholoroquine alone (N=197), those receiving hydroxycholoroquine+azithromycin (N=94), and those receiving neither (controls) (N=92). After adjusting for a number of key confounders (see table) , the use of hydroxycholoroquine+azithromycin was associated with a 66% reduction in risk of death as compared to controls; the analysis also suggested a larger effectiveness of hydroxychloroquine in patients with less severe COVID-19 disease (PO2/FiO2>300, interaction p-value<.0001). Treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalised with COVID-19 Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomised clinical trial Hydroxychloroquine in patients mainly with mild to moderate COVID-19: an open-label, randomised, controlled trial An observational cohort study of hydroxychloroquine and azithromycin for COVID-19: (Can''t get no) satisfaction abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1201971220306007?v=s5 doi: 10.1016/j.ijid.2020.07.056 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel